1
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Murfuni MS, Prestagiacomo LE, Giuliano A, Gabriele C, Signoretti S, Cuda G, Gaspari M. Evaluation of PAC and FASP Performance: DIA-Based Quantitative Proteomic Analysis. Int J Mol Sci 2024; 25:5141. [PMID: 38791181 PMCID: PMC11121386 DOI: 10.3390/ijms25105141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
The aim of this study was to compare filter-aided sample preparation (FASP) and protein aggregation capture (PAC) starting from a three-species protein mix (Human, Soybean and Pisum sativum) and two different starting amounts (1 and 10 µg). Peptide mixtures were analyzed by data-independent acquisition (DIA) and raw files were processed by three commonly used software: Spectronaut, MaxDIA and DIA-NN. Overall, the highest number of proteins (mean value of 5491) were identified by PAC (10 µg), while the lowest number (4855) was identified by FASP (1 µg). The latter experiment displayed the worst performance in terms of both specificity (0.73) and precision (0.24). Other tested conditions showed better diagnostic accuracy, with specificity values of 0.95-0.99 and precision values between 0.61 and 0.86. In order to provide guidance on the data analysis pipeline, the accuracy diagnostic of three software was investigated: (i) the highest sensitivity was obtained with Spectronaut (median of 0.67) highlighting the ability of Spectronaut to quantify low-abundance proteins, (ii) the best precision value was obtained by MaxDIA (median of 0.84), but with a reduced number of identifications compared to Spectronaut and DIA-NN data, and (iii) the specificity values were similar (between 0.93 and 0.99). The data are available on ProteomeXchange with the identifier PXD044349.
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2
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Gent L, Chiappetta ME, Hesketh S, Palmowski P, Porter A, Bonicelli A, Schwalbe EC, Procopio N. Bone Proteomics Method Optimization for Forensic Investigations. J Proteome Res 2024; 23:1844-1858. [PMID: 38621258 PMCID: PMC11077585 DOI: 10.1021/acs.jproteome.4c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
The application of proteomic analysis to forensic skeletal remains has gained significant interest in improving biological and chronological estimations in medico-legal investigations. To enhance the applicability of these analyses to forensic casework, it is crucial to maximize throughput and proteome recovery while minimizing interoperator variability and laboratory-induced post-translational protein modifications (PTMs). This work compared different workflows for extracting, purifying, and analyzing bone proteins using liquid chromatography with tandem mass spectrometry (LC-MS)/MS including an in-StageTip protocol previously optimized for forensic applications and two protocols using novel suspension-trap technology (S-Trap) and different lysis solutions. This study also compared data-dependent acquisition (DDA) with data-independent acquisition (DIA). By testing all of the workflows on 30 human cortical tibiae samples, S-Trap workflows resulted in increased proteome recovery with both lysis solutions tested and in decreased levels of induced deamidations, and the DIA mode resulted in greater sensitivity and window of identification for the identification of lower-abundance proteins, especially when open-source software was utilized for data processing in both modes. The newly developed S-Trap protocol is, therefore, suitable for forensic bone proteomic workflows and, particularly when paired with DIA mode, can offer improved proteomic outcomes and increased reproducibility, showcasing its potential in forensic proteomics and contributing to achieving standardization in bone proteomic analyses for forensic applications.
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Affiliation(s)
- Luke Gent
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Maria Elena Chiappetta
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
- Department
of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Arcavacata
di Rende 87036, Italy
| | - Stuart Hesketh
- School
of Medicine, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Pawel Palmowski
- NUPPA
Facility, Medical School, Newcastle University, Newcastle Upon Tyne NE1
7RU, United Kingdom
| | - Andrew Porter
- NUPPA
Facility, Medical School, Newcastle University, Newcastle Upon Tyne NE1
7RU, United Kingdom
| | - Andrea Bonicelli
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Edward C. Schwalbe
- Department
of Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1
8ST, United Kingdom
| | - Noemi Procopio
- School
of Law and Policing, Research Centre for Field Archaeology and Forensic
Taphonomy, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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3
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Ha A, Khoo A, Ignatchenko V, Khan S, Waas M, Vesprini D, Liu SK, Nyalwidhe JO, Semmes OJ, Boutros PC, Kislinger T. Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine. J Proteome Res 2024; 23:1768-1778. [PMID: 38580319 PMCID: PMC11077481 DOI: 10.1021/acs.jproteome.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited consensus on DIA-MS data analysis approaches for analyzing large numbers of biofluids. To evaluate various DIA-MS workflows, we collected urine from a clinically heterogeneous cohort of prostate cancer patients and acquired data in DDA and DIA scan modes. We then searched the DIA data against urine spectral libraries generated using common library generation approaches or a library-free method. We show that DIA-MS doubles the sample throughput compared to standard DDA-MS with minimal losses to peptide detection. We further demonstrate that using a sample-specific spectral library generated from individual urines maximizes peptide detection compared to a library-free approach, a pan-human library, or libraries generated from pooled, fractionated urines. Adding urine subproteomes, such as the urinary extracellular vesicular proteome, to the urine spectral library further improves the detection of prostate proteins in unfractionated urine. Altogether, we present an optimized DIA-MS workflow and provide several high-quality, comprehensive prostate cancer urine spectral libraries that can streamline future biomarker discovery studies of prostate cancer using DIA-MS.
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Affiliation(s)
- Annie Ha
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Amanda Khoo
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Shahbaz Khan
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Matthew Waas
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Danny Vesprini
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Stanley K. Liu
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Julius O. Nyalwidhe
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Oliver John Semmes
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Paul C. Boutros
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Urology, University of California, Los
Angeles, Los Angeles, California 90095, United States
- Institute
for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Stem Cell Research Center, University of California, Los
Angeles, California 90095, United States
- Broad
Stem Cell Research Center, University of
California, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90024, United States
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Thomas Kislinger
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
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4
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Li S, Luo H, Tang P, Tian C, Hu J, Lu H, Shui W. Generation of a Deep Mouse Brain Spectral Library for Transmembrane Proteome Profiling in Mental Disease Models. Mol Cell Proteomics 2024; 23:100777. [PMID: 38670310 PMCID: PMC11137342 DOI: 10.1016/j.mcpro.2024.100777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024] Open
Abstract
Transmembrane (TM) proteins constitute over 30% of the mammalian proteome and play essential roles in mediating cell-cell communication, synaptic transmission, and plasticity in the central nervous system. Many of these proteins, especially the G protein-coupled receptors (GPCRs), are validated or candidate drug targets for therapeutic development for mental diseases, yet their expression profiles are underrepresented in most global proteomic studies. Herein, we establish a brain TM protein-enriched spectral library based on 136 data-dependent acquisition runs acquired from various brain regions of both naïve mice and mental disease models. This spectral library comprises 3043 TM proteins including 171 GPCRs, 231 ion channels, and 598 transporters. Leveraging this library, we analyzed the data-independent acquisition data from different brain regions of two mouse models exhibiting depression- or anxiety-like behaviors. By integrating multiple informatics workflows and library sources, our study significantly expanded the mental stress-perturbed TM proteome landscape, from which a new GPCR regulator of depression was verified by in vivo pharmacological testing. In summary, we provide a high-quality mouse brain TM protein spectral library to largely increase the TM proteome coverage in specific brain regions, which would catalyze the discovery of new potential drug targets for the treatment of mental disorders.
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Affiliation(s)
- Shanshan Li
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, China; iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Huoqing Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China; Department of Anesthesiology & Perioperative Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Pan Tang
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Cuiping Tian
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Ji Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Haojie Lu
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, China.
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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5
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Kotimoole CN, Ramya VK, Kaur P, Reiling N, Shandil RK, Narayanan S, Flo TH, Prasad TSK. Discovery of Species-Specific Proteotypic Peptides To Establish a Spectral Library Platform for Identification of Nontuberculosis Mycobacteria from Mass Spectrometry-Based Proteomics. J Proteome Res 2024; 23:1102-1117. [PMID: 38358903 DOI: 10.1021/acs.jproteome.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Nontuberculous mycobacteria are opportunistic bacteria pulmonary and extra-pulmonary infections in humans that closely resemble Mycobacterium tuberculosis. Although genome sequencing strategies helped determine NTMs, a common assay for the detection of coinfection by multiple NTMs with M. tuberculosis in the primary attempt of diagnosis is still elusive. Such a lack of efficiency leads to delayed therapy, an inappropriate choice of drugs, drug resistance, disease complications, morbidity, and mortality. Although a high-resolution LC-MS/MS-based multiprotein panel assay can be developed due to its specificity and sensitivity, it needs a library of species-specific peptides as a platform. Toward this, we performed an analysis of proteomes of 9 NTM species with more than 20 million peptide spectrum matches gathered from 26 proteome data sets. Our metaproteomic analyses determined 48,172 species-specific proteotypic peptides across 9 NTMs. Notably, M. smegmatis (26,008), M. abscessus (12,442), M. vaccae (6487), M. fortuitum (1623), M. avium subsp. paratuberculosis (844), M. avium subsp. hominissuis (580), and M. marinum (112) displayed >100 species-specific proteotypic peptides. Finally, these peptides and corresponding spectra have been compiled into a spectral library, FASTA, and JSON formats for future reference and validation in clinical cohorts by the biomedical community for further translation.
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Affiliation(s)
- Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Vadageri Krishnamurthy Ramya
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Parvinder Kaur
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, D-23845 Borstel, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - Radha Krishan Shandil
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Shridhar Narayanan
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Kunnskapssenteret, Øya 424.04.035, Norway
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6
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Langan LM, Lovin LM, Taylor RB, Scarlett KR, Kevin Chambliss C, Chatterjee S, Scott JT, Brooks BW. Proteome changes in larval zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) exposed to (±) anatoxin-a. ENVIRONMENT INTERNATIONAL 2024; 185:108514. [PMID: 38394915 DOI: 10.1016/j.envint.2024.108514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Anatoxin-a and its analogues are potent neurotoxins produced by several genera of cyanobacteria. Due in part to its high toxicity and potential presence in drinking water, these toxins pose threats to public health, companion animals and the environment. It primarily exerts toxicity as a cholinergic agonist, with high affinity at neuromuscular junctions, but molecular mechanisms by which it elicits toxicological responses are not fully understood. To advance understanding of this cyanobacteria, proteomic characterization (DIA shotgun proteomics) of two common fish models (zebrafish and fathead minnow) was performed following (±) anatoxin-a exposure. Specifically, proteome changes were identified and quantified in larval fish exposed for 96 h (0.01-3 mg/L (±) anatoxin-a and caffeine (a methodological positive control) with environmentally relevant treatment levels examined based on environmental exposure distributions of surface water data. Proteomic concentration - response relationships revealed 48 and 29 proteins with concentration - response relationships curves for zebrafish and fathead minnow, respectively. In contrast, the highest number of differentially expressed proteins (DEPs) varied between zebrafish (n = 145) and fathead minnow (n = 300), with only fatheads displaying DEPs at all treatment levels. For both species, genes associated with reproduction were significantly downregulated, with pathways analysis that broadly clustered genes into groups associated with DNA repair mechanisms. Importantly, significant differences in proteome response between the species was also observed, consistent with prior observations of differences in response using both behavioral assays and gene expression, adding further support to model specific differences in organismal sensitivity and/or response. When DEPs were read across from humans to zebrafish, disease ontology enrichment identified diseases associated with cognition and muscle weakness consistent with the prior literature. Our observations highlight limited knowledge of how (±) anatoxin-a, a commonly used synthetic racemate surrogate, elicits responses at a molecular level and advances its toxicological understanding.
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Affiliation(s)
- Laura M Langan
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Environmental Health Sciences, University of South Carolina, Columbia, SC 29208, USA.
| | - Lea M Lovin
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Raegyn B Taylor
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Chemistry, Baylor University, Waco, TX 76798, USA
| | - Kendall R Scarlett
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA
| | - C Kevin Chambliss
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Chemistry, Baylor University, Waco, TX 76798, USA
| | - Saurabh Chatterjee
- Department of Medicine, Department of Environmental and Occupational Health, University of California Irvine, Irvine, CA 92617, USA
| | - J Thad Scott
- Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA; Department of Biology, Baylor University, Waco, TX 76798, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, Waco, TX 76798, USA.
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7
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Liu W, Wen Z, Shi Y, Bao J, Ma S, Liang J. Research progress in the application of proteomics technology in brain injury. Biomed Chromatogr 2024; 38:e5785. [PMID: 38014505 DOI: 10.1002/bmc.5785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023]
Abstract
The aim of this article is to review the application progress of proteomics technology in brain injury research in recent years, point out the current problems that need to be overcome, and explore the application prospects of proteomics analysis in brain injury. This study also aims to retrieve all literature on brain injury and proteomics and summarize it. Through searching and screening, the widespread application of proteomics technology in the treatment of traumatic brain injury (TBI) and the use of a large number of TBI biomarkers were discovered. The pathways mediated by some biomarkers and the physiological and pathological mechanisms of occurrence were elucidated. The current classification of brain injury is mainly based on subjective evaluation of clinical symptoms, combined with objective imaging. However, its practical value is often limited when applied to prognosis evaluation in brain injury. Proteomics technology can make up for this deficiency and provide a reference for the prevention and treatment of brain injury.
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Affiliation(s)
- Wenhu Liu
- The First Clinical Medical College of Gansu University of Traditional Chinese Medicine, Lanzhou City, People's Republic of China
| | - Zhaomeng Wen
- The First Clinical Medical College of Gansu University of Traditional Chinese Medicine, Lanzhou City, People's Republic of China
| | - Yuwei Shi
- The First Clinical Medical College of Gansu University of Traditional Chinese Medicine, Lanzhou City, People's Republic of China
| | - Juan Bao
- Department of Neurosurgery, Gansu Provincial Hospital, Lanzhou City, People's Republic of China
| | - Shaobo Ma
- Department of Neurosurgery, Gansu Provincial Hospital, Lanzhou City, People's Republic of China
| | - Jin Liang
- Department of Neurosurgery, Gansu Provincial Hospital, Lanzhou City, People's Republic of China
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8
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Fields L, Ma M, DeLaney K, Phetsanthad A, Li L. A crustacean neuropeptide spectral library for data-independent acquisition (DIA) mass spectrometry applications. Proteomics 2024:e2300285. [PMID: 38171828 DOI: 10.1002/pmic.202300285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
Neuropeptides have tremendous potential for application in modern medicine, including utility as biomarkers and therapeutics. To overcome the inherent challenges associated with neuropeptide identification and characterization, data-independent acquisition (DIA) is a fitting mass spectrometry (MS) method of choice to achieve sensitive and accurate analysis. It is advantageous for preliminary neuropeptidomic studies to occur in less complex organisms, with crustacean models serving as a popular choice due to their relatively simple nervous system. With spectral libraries serving as a means to interpret DIA-MS output spectra, and Cancer borealis as a model of choice for neuropeptide analysis, we performed the first spectral library mapping of crustacean neuropeptides. Leveraging pre-existing data-dependent acquisition (DDA) spectra, a spectral library was built using PEAKS Online. The library is comprised of 333 unique neuropeptides. The identification results obtained through the use of this spectral library were compared with those achieved through library-free analysis of crustacean brain, pericardial organs (PO), and thoracic ganglia (TG) tissues. A statistically significant increase (Student's t-test, P value < 0.05) in the number of identifications achieved from the TG data was observed in the spectral library results. Furthermore, in each of the tissues, a distinctly different set of identifications was found in the library search compared to the library-free search. This work highlights the necessity for the use of spectral libraries in neuropeptide analysis, illustrating the advantage of spectral libraries for interpreting DIA spectra in a reproducible manner with greater neuropeptidomic depth.
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Affiliation(s)
- Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Oh YH, Mendola KM, Choe LH, Min L, Lavoie AR, Sripada SA, Williams TI, Lee KH, Yigzaw Y, Seay A, Bill J, Li X, Roush DJ, Cramer SM, Menegatti S, Lenhoff AM. Identification and characterization of CHO host-cell proteins in monoclonal antibody bioprocessing. Biotechnol Bioeng 2024; 121:291-305. [PMID: 37877536 PMCID: PMC10842603 DOI: 10.1002/bit.28568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/23/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023]
Abstract
Host-cell proteins (HCPs) are the foremost class of process-related impurities to be controlled and removed in downstream processing steps in monoclonal antibody (mAb) manufacturing. However, some HCPs may evade clearance in multiple purification steps and reach the final drug product, potentially threatening drug stability and patient safety. This study extends prior work on HCP characterization and persistence in mAb process streams by using mass spectrometry (MS)-based methods to track HCPs through downstream processing steps for seven mAbs that were generated by five different cell lines. The results show considerable variability in HCP identities in the processing steps but extensive commonality in the identities and quantities of the most abundant HCPs in the harvests for different processes. Analysis of HCP abundance in the harvests shows a likely relationship between abundance and the reproducibility of quantification measurements and suggests that some groups of HCPs may hinder the characterization. Quantitative monitoring of HCPs persisting through purification steps coupled with the findings from the harvest analysis suggest that multiple factors, including HCP abundance and mAb-HCP interactions, can contribute to the persistence of individual HCPs and the identification of groups of common, persistent HCPs in mAb manufacturing.
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Affiliation(s)
- Young Hoon Oh
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Kerri M Mendola
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Leila H Choe
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Lie Min
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Ashton R Lavoie
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Sobhana A Sripada
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Taufika Islam Williams
- Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina, USA
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Yinges Yigzaw
- Purification Process Development, Genentech, Inc., South San Francisco, California, USA
| | - Alexander Seay
- Purification Process Development, Genentech, Inc., South San Francisco, California, USA
| | - Jerome Bill
- Purification Process Development, Genentech, Inc., South San Francisco, California, USA
| | - Xuanwen Li
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - David J Roush
- BPR&D, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Steven M Cramer
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
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10
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Van Bael S, Ludwig C, Baggerman G, Temmerman L. Identification and Targeted Quantification of Endogenous Neuropeptides in the Nematode Caenorhabditis elegans Using Mass Spectrometry. Methods Mol Biol 2024; 2758:341-373. [PMID: 38549024 DOI: 10.1007/978-1-0716-3646-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The nematode Caenorhabditis elegans lends itself as an excellent model organism for peptidomics studies. Its ease of cultivation and quick generation time make it suitable for high-throughput studies. The nervous system, with its 302 neurons, is probably the best-known and studied endocrine tissue. Moreover, its neuropeptidergic signaling pathways display numerous similarities with those observed in other metazoans. Here, we describe two label-free approaches for neuropeptidomics in C. elegans: one for discovery purposes, and another for targeted quantification and comparisons of neuropeptide levels between different samples. Starting from a detailed peptide extraction procedure, we here outline the liquid chromatography tandem mass spectrometry (LC-MS/MS) setup and describe subsequent data analysis approaches.
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Affiliation(s)
- Sven Van Bael
- Department of Biology, Animal Physiology & Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Geert Baggerman
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Liesbet Temmerman
- Department of Biology, Animal Physiology & Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium.
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11
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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2023:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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12
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Gacem S, Castello-Ruiz M, Hidalgo CO, Tamargo C, Santolaria P, Soler C, Yániz JL, Silvestre MA. Bull Sperm SWATH-MS-Based Proteomics Reveals Link between High Fertility and Energy Production, Motility Structures, and Sperm-Oocyte Interaction. J Proteome Res 2023; 22:3607-3624. [PMID: 37782577 PMCID: PMC10629479 DOI: 10.1021/acs.jproteome.3c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 10/04/2023]
Abstract
The prediction of male or semen fertility potential remains a persistent challenge that has yet to be fully resolved. This work analyzed several in vitro parameters and proteome of spermatozoa in bulls cataloged as high- (HF; n = 5) and low-field (LF; n = 5) fertility after more than a thousand artificial inseminations. Sperm motility was evaluated by computer-assisted sperm analysis. Sperm viability, mitochondrial membrane potential (MMP) and reactive oxygen species (mROS) of spermatozoa were assessed by flow cytometry. Proteome was evaluated by the SWATH-MS procedure. Spermatozoa of HF bulls showed significantly higher total motility than the LF group (41.4% vs 29.7%). Rates of healthy sperm (live, high MMP, and low mROS) for HF and LF bull groups were 49% and 43%, respectively (p > 0.05). Spermatozoa of HF bulls showed a higher presence of differentially abundant proteins (DAPs) related to both energy production (COX7C), mainly the OXPHOS pathway, and the development of structures linked with the motility process (TPPP2, SSMEM1, and SPAG16). Furthermore, we observed that equatorin (EQTN), together with other DAPs related to the interaction with the oocyte, was overrepresented in HF bull spermatozoa. The biological processes related to protein processing, catabolism, and protein folding were found to be overrepresented in LF bull sperm in which the HSP90AA1 chaperone was identified as the most DAP. Data are available via ProteomeXchange with identifier PXD042286.
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Affiliation(s)
- Sabrina Gacem
- Departamento
de Biología Celular, Biología Funcional y Antropología
Física, Universitat de València, 46100 Valencia, Spain
- Departamento
de Medicina y Cirugía Animal, Universitat
Autònoma de Barcelona, 08193 Barcelona, Spain
| | - María Castello-Ruiz
- Departamento
de Biología Celular, Biología Funcional y Antropología
Física, Universitat de València, 46100 Valencia, Spain
- Unidad
Mixta de Investigación Cerebrovascular, Instituto de Investigación
Sanitaria La Fe, Hospital Universitario
y Politécnico La Fe, 46026 Valencia, Spain
| | - Carlos O. Hidalgo
- Animal
Selection and Reproduction Area, Regional
Agrifood Research and Development Service (SERIDA), 33394 Deva, Gijón, Spain
| | - Carolina Tamargo
- Animal
Selection and Reproduction Area, Regional
Agrifood Research and Development Service (SERIDA), 33394 Deva, Gijón, Spain
| | - Pilar Santolaria
- BIOFITER
Research Group, Institute of Environmental Sciences (IUCA), University of Zaragoza, 22071 Huesca, Spain
| | - Carles Soler
- Departamento
de Biología Celular, Biología Funcional y Antropología
Física, Universitat de València, 46100 Valencia, Spain
| | - Jesús L. Yániz
- BIOFITER
Research Group, Institute of Environmental Sciences (IUCA), University of Zaragoza, 22071 Huesca, Spain
| | - Miguel A. Silvestre
- Departamento
de Biología Celular, Biología Funcional y Antropología
Física, Universitat de València, 46100 Valencia, Spain
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13
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Huang J, Staes A, Impens F, Demichev V, Van Breusegem F, Gevaert K, Willems P. CysQuant: Simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry. Redox Biol 2023; 67:102908. [PMID: 37793239 PMCID: PMC10562924 DOI: 10.1016/j.redox.2023.102908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function. Accurate quantification of cysteine oxidation is therefore crucial for decoding protein redox regulation. Here, we present CysQuant, a novel approach for simultaneous quantification of cysteine oxidation degrees and protein abundancies. CysQuant involves light/heavy iodoacetamide isotopologues for differential labeling of reduced and reversibly oxidized cysteines analyzed by data-dependent acquisition (DDA) or data-independent acquisition mass spectrometry (DIA-MS). Using plexDIA with in silico predicted spectral libraries, we quantified an average of 18% cysteine oxidation in Arabidopsis thaliana by DIA-MS, including a subset of highly oxidized cysteines forming disulfide bridges in AlphaFold2 predicted structures. Applying CysQuant to Arabidopsis seedlings exposed to excessive light, we successfully quantified the well-established increased reduction of Calvin-Benson cycle enzymes and discovered yet uncharacterized redox-sensitive disulfides in chloroplastic enzymes. Overall, CysQuant is a highly versatile tool for assessing the cysteine modification status that can be widely applied across various mass spectrometry platforms and organisms.
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Affiliation(s)
- Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - An Staes
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium; VIB Proteomics Core, 9052, Ghent, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium; VIB Proteomics Core, 9052, Ghent, Belgium
| | - Vadim Demichev
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
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14
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Phipps WS, Kilgore MR, Kennedy JJ, Whiteaker JR, Hoofnagle AN, Paulovich AG. Clinical Proteomics for Solid Organ Tissues. Mol Cell Proteomics 2023; 22:100648. [PMID: 37730181 PMCID: PMC10692389 DOI: 10.1016/j.mcpro.2023.100648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023] Open
Abstract
The evaluation of biopsied solid organ tissue has long relied on visual examination using a microscope. Immunohistochemistry is critical in this process, labeling and detecting cell lineage markers and therapeutic targets. However, while the practice of immunohistochemistry has reshaped diagnostic pathology and facilitated improvements in cancer treatment, it has also been subject to pervasive challenges with respect to standardization and reproducibility. Efforts are ongoing to improve immunohistochemistry, but for some applications, the benefit of such initiatives could be impeded by its reliance on monospecific antibody-protein reagents and limited multiplexing capacity. This perspective surveys the relevant challenges facing traditional immunohistochemistry and describes how mass spectrometry, particularly liquid chromatography-tandem mass spectrometry, could help alleviate problems. In particular, targeted mass spectrometry assays could facilitate measurements of individual proteins or analyte panels, using internal standards for more robust quantification and improved interlaboratory reproducibility. Meanwhile, untargeted mass spectrometry, showcased to date clinically in the form of amyloid typing, is inherently multiplexed, facilitating the detection and crude quantification of 100s to 1000s of proteins in a single analysis. Further, data-independent acquisition has yet to be applied in clinical practice, but offers particular strengths that could appeal to clinical users. Finally, we discuss the guidance that is needed to facilitate broader utilization in clinical environments and achieve standardization.
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Affiliation(s)
- William S Phipps
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark R Kilgore
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jacob J Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA; Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.
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15
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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16
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Hay BN, Akinlaja MO, Baker TC, Houfani AA, Stacey RG, Foster LJ. Integration of data-independent acquisition (DIA) with co-fractionation mass spectrometry (CF-MS) to enhance interactome mapping capabilities. Proteomics 2023; 23:e2200278. [PMID: 37144656 DOI: 10.1002/pmic.202200278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Proteomics technologies are continually advancing, providing opportunities to develop stronger and more robust protein interaction networks (PINs). In part, this is due to the ever-growing number of high-throughput proteomics methods that are available. This review discusses how data-independent acquisition (DIA) and co-fractionation mass spectrometry (CF-MS) can be integrated to enhance interactome mapping abilities. Furthermore, integrating these two techniques can improve data quality and network generation through extended protein coverage, less missing data, and reduced noise. CF-DIA-MS shows promise in expanding our knowledge of interactomes, notably for non-model organisms (NMOs). CF-MS is a valuable technique on its own, but upon the integration of DIA, the potential to develop robust PINs increases, offering a unique approach for researchers to gain an in-depth understanding into the dynamics of numerous biological processes.
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Affiliation(s)
- Brenna N Hay
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Mopelola O Akinlaja
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Teesha C Baker
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Aicha Asma Houfani
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - R Greg Stacey
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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17
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Gupta S, Sing JC, Röst HL. Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment. Commun Biol 2023; 6:1101. [PMID: 37903988 PMCID: PMC10616189 DOI: 10.1038/s42003-023-05437-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
DIA is a mainstream method for quantitative proteomics, but consistent quantification across multiple LC-MS/MS instruments remains a bottleneck in parallelizing data acquisition. One reason for this inconsistency and missing quantification is the retention time shift which current software does not adequately address for runs from multiple sites. We present multirun chromatogram alignment strategies to map peaks across columns, including the traditional reference-based Star method, and two novel approaches: MST and Progressive alignment. These reference-free strategies produce a quantitatively accurate data-matrix, even from heterogeneous multi-column studies. Progressive alignment also generates merged chromatograms from all runs which has not been previously achieved for LC-MS/MS data. First, we demonstrate the effectiveness of multirun alignment strategies on a gold-standard annotated dataset, resulting in a threefold reduction in quantitation error-rate compared to non-aligned DIA results. Subsequently, on a multi-species dataset that DIAlignR effectively controls the quantitative error rate, improves precision in protein measurements, and exhibits conservative peak alignment. We next show that the MST alignment reduces cross-site CV by 50% for highly abundant proteins when applied to a dataset from 11 different LC-MS/MS setups. Finally, the reanalysis of 949 plasma runs with multirun alignment revealed a more than 50% increase in insulin resistance (IR) and respiratory viral infection (RVI) proteins, identifying 11 and 13 proteins respectively, compared to prior analysis without it. The three strategies are implemented in our DIAlignR workflow (>2.3) and can be combined with linear, non-linear, or hybrid pairwise alignment.
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Affiliation(s)
- Shubham Gupta
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Justin C Sing
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hannes L Röst
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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18
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Stepler KE, Hannah SC, Taneyhill LA, Nemes P. Deep Proteome of the Developing Chick Midbrain. J Proteome Res 2023; 22:3264-3274. [PMID: 37616547 DOI: 10.1021/acs.jproteome.3c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The epithelial-to-mesenchymal transition (EMT) and migration of cranial neural crest cells within the midbrain are critical processes that permit proper craniofacial patterning in the early embryo. Disruptions in these processes not only impair development but also lead to various diseases, underscoring the need for their detailed understanding at the molecular level. The chick embryo has served historically as an excellent model for human embryonic development, including cranial neural crest cell EMT and migration. While these developmental events have been characterized transcriptionally, studies at the protein level have not been undertaken to date. Here, we applied mass spectrometry (MS)-based proteomics to establish a deep proteomics profile of the chick midbrain region during early embryonic development. Our proteomics method combines optimal lysis conditions, offline fractionation, separation on a nanopatterned stationary phase (μPAC) using nanoflow liquid chromatography, and detection using quadrupole-ion trap-Orbitrap tribrid high-resolution tandem MS. Identification of >5900 proteins and >450 phosphoproteins in this study marks the deepest coverage of the chick midbrain proteome to date. These proteins have known roles in pathways related to neural crest cell EMT and migration such as signaling, proteolysis/extracellular matrix remodeling, and transcriptional regulation. This study offers valuable insight into important developmental processes occurring in the midbrain region and demonstrates the utility of proteomics for characterization of tissue microenvironments during chick embryogenesis.
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Affiliation(s)
- Kaitlyn E Stepler
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Seth C Hannah
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Lisa A Taneyhill
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland 20742, United States
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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19
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Teunissen CE, Kimble L, Bayoumy S, Bolsewig K, Burtscher F, Coppens S, Das S, Gogishvili D, Fernandes Gomes B, Gómez de San José N, Mavrina E, Meda FJ, Mohaupt P, Mravinacová S, Waury K, Wojdała AL, Abeln S, Chiasserini D, Hirtz C, Gaetani L, Vermunt L, Bellomo G, Halbgebauer S, Lehmann S, Månberg A, Nilsson P, Otto M, Vanmechelen E, Verberk IMW, Willemse E, Zetterberg H. Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias. Mol Cell Proteomics 2023; 22:100629. [PMID: 37557955 PMCID: PMC10594029 DOI: 10.1016/j.mcpro.2023.100629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Neurodegenerative dementias are progressive diseases that cause neuronal network breakdown in different brain regions often because of accumulation of misfolded proteins in the brain extracellular matrix, such as amyloids or inside neurons or other cell types of the brain. Several diagnostic protein biomarkers in body fluids are being used and implemented, such as for Alzheimer's disease. However, there is still a lack of biomarkers for co-pathologies and other causes of dementia. Such biofluid-based biomarkers enable precision medicine approaches for diagnosis and treatment, allow to learn more about underlying disease processes, and facilitate the development of patient inclusion and evaluation tools in clinical trials. When designing studies to discover novel biofluid-based biomarkers, choice of technology is an important starting point. But there are so many technologies to choose among. To address this, we here review the technologies that are currently available in research settings and, in some cases, in clinical laboratory practice. This presents a form of lexicon on each technology addressing its use in research and clinics, its strengths and limitations, and a future perspective.
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Affiliation(s)
- Charlotte E Teunissen
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands.
| | - Leighann Kimble
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; KIN Center for Digital Innovation, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sherif Bayoumy
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Katharina Bolsewig
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Felicia Burtscher
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Salomé Coppens
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; National Measurement Laboratory at LGC, Teddington, United Kingdom
| | - Shreyasee Das
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; ADx NeuroSciences, Gent, Belgium
| | - Dea Gogishvili
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Bárbara Fernandes Gomes
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Nerea Gómez de San José
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany
| | - Ekaterina Mavrina
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; KIN Center for Digital Innovation, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Francisco J Meda
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Pablo Mohaupt
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Sára Mravinacová
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Katharina Waury
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Anna Lidia Wojdała
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Sanne Abeln
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Davide Chiasserini
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Physiology and Biochemistry, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Christophe Hirtz
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Lorenzo Gaetani
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Lisa Vermunt
- Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Giovanni Bellomo
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Steffen Halbgebauer
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany; German Center for Neurodegenerative Diseases (DZNE e.V.), Ulm, Germany
| | - Sylvain Lehmann
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Anna Månberg
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Peter Nilsson
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Markus Otto
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany; Department of Neurology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Eugeen Vanmechelen
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; ADx NeuroSciences, Gent, Belgium
| | - Inge M W Verberk
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Eline Willemse
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Henrik Zetterberg
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK; Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China; Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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20
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Zhang X, Ruan C, Wang Y, Wang K, Liu X, Lyu J, Ye M. Integrated Protein Solubility Shift Assays for Comprehensive Drug Target Identification on a Proteome-Wide Scale. Anal Chem 2023; 95:13779-13787. [PMID: 37676971 DOI: 10.1021/acs.analchem.3c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Target proteins are often stabilized after binding with a ligand and thereby typically become more resistant to denaturation. Based on this phenomenon, several methods without the need to covalently modify the ligand have been developed to identify target proteins for a specific ligand. These methods usually employ complicated workflows with high cost and limited throughput. Here, we develop an iso-pH shift assay (ipHSA) method, a proteome-wide target identification method that detects ligand-induced protein solubility shifts by precipitating proteins with a single concentration of acidic agent followed by protein quantification via data-independent acquisition (DIA). Using a pan-kinase inhibitor, staurosporine, we demonstrated that ipHSA increased throughput compared to the previously developed pH-dependent protein precipitation (pHDPP) method. ipHSA was found to have high complementarity in staurosporine target identification compared with the improved isothermal shift assay (iTSA) and isosolvent shift assay (iSSA) using DIA instead of tandem mass tags (TMTs) for quantification. To further improve target identification sensitivity, we developed an integrated protein solubility shift assay (IPSSA) by pooling the supernatants yielded from ipHSA, iTSA, and iSSA methods. IPSSA exhibited increased sensitivity in screening staurosporine targets by 38, 29, and 38% compared to individual methods. Increasing the number of replicate experiments further enhanced the sensitivity of target identification. Meanwhile, IPSSA also improved the throughput and reduced the cost compared with previous methods. As a fast and efficient tool for drug target identification, IPSSA is expected to have broad applications in the study of the mechanism of action.
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Affiliation(s)
- Xiaolei Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chengfei Ruan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Yang C, Yang L, Yang L, Li S, Ye L, Ye J, Chen C, Zeng Y, Zhu M, Lin X, Peng Q, Wang Y, Jin M. Plasma Proteomics Study Between the Frequent Exacerbation and Infrequent Exacerbation Phenotypes of Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2023; 18:1713-1728. [PMID: 37581107 PMCID: PMC10423573 DOI: 10.2147/copd.s408361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/09/2023] [Indexed: 08/16/2023] Open
Abstract
Background Frequent exacerbation (FE) and infrequent exacerbation (IE) are two phenotypes of chronic obstructive pulmonary disease (COPD), of which FE is associated with a higher incidence of exacerbation and a serious threat to human health. Because the pathogenesis mechanisms of FE are unclear, this study aims to identify FE-related proteins in the plasma via proteomics for use as predictive, diagnostic, and therapeutic biomarkers of COPD. Methods A cross-sectional study was conducted in which plasma protein profiles were analyzed in COPD patients at stable stage, and differentially expressed proteins (DEPs) were screened out between the FE and IE patients. FE-related DEPs were identified using data-independent acquisition-based proteomics and bioinformatics analyses. In addition, FE-related candidates were verified by enzyme-linked immunosorbent assay. Results In this study, 47 DEPs were screened out between the FE and IE groups, including 20 upregulated and 27 downregulated proteins. Key biological functions (eg, neutrophil degranulation, extracellular exosome, protein homodimerization activity) and signaling pathways (eg, arginine and proline metabolism) were enriched in association with the FE phenotype. Receiver operating characteristic (ROC) analysis of the 11 combined DEPs revealed an area under the curve of 0.985 (p <0.05) for discriminating FE from IE. Moreover, correlation and ROC curve analyses indicated that creatine kinase, M-type (CKM) and fat storage-inducing transmembrane protein 1 (FITM1) might be clinically significant in patients with the FE phenotype. In addition, plasma expression levels of CKM and FITM1 were validated to be significantly decreased in the FE group compared with the IE group (CKM: p <0.01; FITM1: p <0.05). Conclusion In this study, novel insights into COPD pathogenesis were provided by investigating and comparing plasma protein profiles between the FE and IE patients. CKM, FITM1, and a combinative biomarker panel may serve as useful tools for assisting in the precision diagnosis and effective treatment of the FE phenotype of COPD.
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Affiliation(s)
- Chengyu Yang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Huadong Hospital, Fudan University, Shanghai, 200040, People’s Republic of China
| | - Li Yang
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
- Key Laboratory of Interventional Pulmonology of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
| | - Lei Yang
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
| | - Shuiming Li
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
| | - Ling Ye
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
- Department of Allergy, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Jinfeng Ye
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
| | - Chengshui Chen
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
- Key Laboratory of Interventional Pulmonology of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, the Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital, Zhejiang, 324000, People’s Republic of China
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, the Second Affiliated Hospital of Fujian Medical University, Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian, 362000, People’s Republic of China
| | - Mengchan Zhu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Xiaoping Lin
- Department of Pulmonary and Critical Care Medicine, the Second Affiliated Hospital of Fujian Medical University, Respiratory Medicine Center of Fujian Province, Quanzhou, Fujian, 362000, People’s Republic of China
| | - Qing Peng
- Department of Pulmonary and Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, 201199, People’s Republic of China
| | - Yun Wang
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, Guangdong, 518055, People’s Republic of China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, People’s Republic of China
| | - Meiling Jin
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
- Department of Allergy, Zhongshan Hospital, Fudan University, Shanghai, 200032, People’s Republic of China
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22
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George AL, Sidgwick FR, Watt JE, Martin MP, Trost M, Marín-Rubio JL, Dueñas ME. Comparison of Quantitative Mass Spectrometric Methods for Drug Target Identification by Thermal Proteome Profiling. J Proteome Res 2023; 22:2629-2640. [PMID: 37439223 PMCID: PMC10407934 DOI: 10.1021/acs.jproteome.3c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Indexed: 07/14/2023]
Abstract
Thermal proteome profiling (TPP) provides a powerful approach to studying proteome-wide interactions of small therapeutic molecules and their target and off-target proteins, complementing phenotypic-based drug screens. Detecting differences in thermal stability due to target engagement requires high quantitative accuracy and consistent detection. Isobaric tandem mass tags (TMTs) are used to multiplex samples and increase quantification precision in TPP analysis by data-dependent acquisition (DDA). However, advances in data-independent acquisition (DIA) can provide higher sensitivity and protein coverage with reduced costs and sample preparation steps. Herein, we explored the performance of different DIA-based label-free quantification approaches compared to TMT-DDA for thermal shift quantitation. Acute myeloid leukemia cells were treated with losmapimod, a known inhibitor of MAPK14 (p38α). Label-free DIA approaches, and particularly the library-free mode in DIA-NN, were comparable of TMT-DDA in their ability to detect target engagement of losmapimod with MAPK14 and one of its downstream targets, MAPKAPK3. Using DIA for thermal shift quantitation is a cost-effective alternative to labeled quantitation in the TPP pipeline.
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Affiliation(s)
- Amy L. George
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Frances R. Sidgwick
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Jessica E. Watt
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Mathew P. Martin
- Newcastle
Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Matthias Trost
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - José Luis Marín-Rubio
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Maria Emilia Dueñas
- Laboratory
for Biological Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, U.K.
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23
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Beaumal C, Beck A, Hernandez-Alba O, Carapito C. Advanced mass spectrometry workflows for accurate quantification of trace-level host cell proteins in drug products: Benefits of FAIMS separation and gas-phase fractionation DIA. Proteomics 2023; 23:e2300172. [PMID: 37148167 DOI: 10.1002/pmic.202300172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/08/2023]
Abstract
Therapeutic monoclonal antibodies (mAb) production relies on multiple purification steps before release as a drug product (DP). A few host cell proteins (HCPs) may co-purify with the mAb. Their monitoring is crucial due to the considerable risk they represent for mAb stability, integrity, and efficacy and their potential immunogenicity. Enzyme-linked immunosorbent assays (ELISA) commonly used for global HCP monitoring present limitations in terms of identification and quantification of individual HCPs. Therefore, liquid chromatography tandem mass spectrometry (LC-MS/MS) has emerged as a promising alternative. Challenging DP samples show an extreme dynamic range requiring high performing methods to detect and reliably quantify trace-level HCPs. Here, we investigated the benefits of adding high-field asymmetric ion mobility spectrometry (FAIMS) separation and gas phase fractionation (GPF) prior to data independent acquisition (DIA). FAIMS LC-MS/MS analysis allowed the identification of 221 HCPs among which 158 were reliably quantified for a global amount of 880 ng/mg of NIST mAb Reference Material. Our methods have also been successfully applied to two FDA/EMA approved DPs and allowed digging deeper into the HCP landscape with the identification and quantification of a few tens of HCPs with sensitivity down to the sub-ng/mg of mAb level.
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Affiliation(s)
- Corentin Beaumal
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Alain Beck
- IRPF, Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, CNRS, Université de Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
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24
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Yu F, Teo GC, Kong AT, Fröhlich K, Li GX, Demichev V, Nesvizhskii AI. Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform. Nat Commun 2023; 14:4154. [PMID: 37438352 PMCID: PMC10338508 DOI: 10.1038/s41467-023-39869-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we present a fast and sensitive approach for direct peptide identification from DIA data, MSFragger-DIA, which leverages the unmatched speed of the fragment ion indexing-based search engine MSFragger. Different from most existing methods, MSFragger-DIA conducts a database search of the DIA tandem mass (MS/MS) spectra prior to spectral feature detection and peak tracing across the LC dimension. To streamline the analysis of DIA data and enable easy reproducibility, we integrate MSFragger-DIA into the FragPipe computational platform for seamless support of peptide identification and spectral library building from DIA, data-dependent acquisition (DDA), or both data types combined. We compare MSFragger-DIA with other DIA tools, such as DIA-Umpire based workflow in FragPipe, Spectronaut, DIA-NN library-free, and MaxDIA. We demonstrate the fast, sensitive, and accurate performance of MSFragger-DIA across a variety of sample types and data acquisition schemes, including single-cell proteomics, phosphoproteomics, and large-scale tumor proteome profiling studies.
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Affiliation(s)
- Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Andy T Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Klemens Fröhlich
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Vadim Demichev
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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25
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Kirkpatrick J, Stemmer PM, Searle BC, Herring LE, Martin L, Midha MK, Phinney BS, Shan B, Palmblad M, Wang Y, Jagtap PD, Neely BA. 2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study. J Biomol Tech 2023; 34:3fc1f5fe.9b78d780. [PMID: 37435391 PMCID: PMC10332336 DOI: 10.7171/3fc1f5fe.9b78d780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in proteomics core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluate DIA performance in proteomics laboratories with various instrumentation. Participants were supplied with generic methods and a uniform set of test samples. The resulting 49 DIA datasets act as benchmarks and have utility in education and tool development. The sample set consisted of a tryptic HeLa digest spiked with high or low levels of 4 exogenous proteins. Data are available in MassIVE MSV000086479. Additionally, we demonstrate how the data can be analyzed by focusing on 2 datasets using different library approaches and show the utility of select summary statistics. These data can be used by DIA newcomers, software developers, or DIA experts evaluating performance with different platforms, acquisition settings, and skill levels.
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Affiliation(s)
- Joanna Kirkpatrick
- Leibniz Institute on AgingFritz Lipmann Institute07745JenaGermany
- The Francis Crick InstituteLondonNW1 1ATUnited Kingdom
| | | | - Brian C. Searle
- Department of Biomedical InformaticsThe Ohio State UniversityColumbusOhio43210USA
- Pelotonia Institute for Immuno-OncologyThe Ohio State University Comprehensive Cancer CenterColumbusOhio43210USA
| | - Laura E. Herring
- UNC Proteomics Core FacilityDepartment of PharmacologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27514USA
| | | | | | | | - Baozhen Shan
- Bioinformatics Solutions Inc.WaterlooON N2L 3K8Canada
| | - Magnus Palmblad
- Center for Proteomics and MetabolomicsLeiden University Medical Center2333 ZC LeidenThe Netherlands
| | - Yan Wang
- National Institute of Dental and Craniofacial ResearchNational Institutes of HealthBethesdaMaryland20892USA
| | - Pratik D. Jagtap
- Department of BiochemistryMolecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMinnesota55455USA
| | - Benjamin A. Neely
- National Institute of Standards and TechnologyCharlestonSouth Carolina29412USA
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26
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Wu X, Liu YK, Iliuk AB, Tao WA. Mass spectrometry-based phosphoproteomics in clinical applications. Trends Analyt Chem 2023; 163:117066. [PMID: 37215489 PMCID: PMC10195102 DOI: 10.1016/j.trac.2023.117066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.
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Affiliation(s)
- Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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27
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Sun W, Lin Y, Huang Y, Chan J, Terrillon S, Rosenbaum AI, Contrepois K. Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition. Mol Cell Proteomics 2023:100562. [PMID: 37142056 DOI: 10.1016/j.mcpro.2023.100562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
Modern mass spectrometers routinely allow deep proteome coverage in a single experiment. These methods are typically operated at nano and micro flow regimes, but they often lack throughput and chromatographic robustness, which is critical for large-scale studies. In this context, we have developed, optimized and benchmarked LC-MS methods combining the robustness and throughput of analytical flow chromatography with the added sensitivity provided by the Zeno trap across a wide range of cynomolgus monkey and human matrices of interest for toxicological studies and clinical biomarker discovery. SWATH data independent acquisition (DIA) experiments with Zeno trap activated (Zeno SWATH DIA) provided a clear advantage over conventional SWATH DIA in all sample types tested with improved sensitivity, quantitative robustness and signal linearity as well as increased protein coverage by up to 9-fold. Using a 10-min gradient chromatography, up to 3,300 proteins were identified in tissues at 2 μg peptide load. Importantly, the performance gains with Zeno SWATH translated into better biological pathway representation and improved the ability to identify dysregulated proteins and pathways associated with two metabolic diseases in human plasma. Finally, we demonstrate that this method is highly stable over time with the acquisition of reliable data over the injection of 1,000+ samples (14.2 days of uninterrupted acquisition) without the need for human intervention or normalization. Altogether, Zeno SWATH DIA methodology allows fast, sensitive and robust proteomic workflows using analytical flow and is amenable to large-scale studies. This work provides detailed method performance assessment on a variety of relevant biological matrices and serves as a valuable resource for the proteomics community.
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Affiliation(s)
- Weiwen Sun
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA 94080, USA
| | - Yuan Lin
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA 94080, USA
| | - Yue Huang
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA 94080, USA
| | - Josolyn Chan
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA 94080, USA
| | - Sonia Terrillon
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA 94080, USA
| | - Anton I Rosenbaum
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA 94080, USA.
| | - Kévin Contrepois
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, South San Francisco, CA 94080, USA.
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28
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Li X, Huang Y, Zheng K, Yu G, Wang Q, Gu L, Li J, Wang H, Zhang W, Sun Y, Li C. Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer. BIOPHYSICS REPORTS 2023; 9:67-81. [PMID: 37753059 PMCID: PMC10518519 DOI: 10.52601/bpr.2022.210048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 11/18/2022] [Indexed: 02/19/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics and phosphoproteomics are powerful methods to study the biological mechanisms, diagnostic biomarkers, prognostic analysis, and drug therapy of tumors. Data-independent acquisition (DIA) mode is considered to perform better than data-dependent acquisition (DDA) mode in terms of quantitative reproducibility, specificity, accuracy, and identification of low-abundance proteins. Mini patient derived xenograft (MiniPDX) model is an effective model to assess the response to antineoplastic drugs in vivo and is helpful for the precise treatment of cancer patients. Kinases are favorable spots for tumor-targeted drugs, and their functional completion relies on signaling pathways through phosphorylating downstream substrates. Kinase-phosphorylation networks or edge interactions are considered more credible and permanent for characterizing complex diseases. Here, we provide a workflow for personalized drug response assessment in primary and metastatic colorectal cancer (CRC) tumors using DIA proteomic data, DIA phosphoproteomic data, and MiniPDX models. Three kinase inhibitors, afatinib, gefitinib, and regorafenib, are tested pharmacologically. The process mainly includes the following steps: clinical tissue collection, sample preparation, hybrid spectral libraries establishment, MS data acquisition, kinase-substrate network construction, in vivo drug test, and elastic regression modeling. Our protocol gives a more direct data basis for individual drug responses, and will improve the selection of treatment strategies for patients without the druggable mutation.
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Affiliation(s)
- Xumiao Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yiming Huang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kuo Zheng
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Guanyu Yu
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Zhang
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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29
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Phetsanthad A, Carr AV, Fields L, Li L. Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides. J Proteome Res 2023; 22:1510-1519. [PMID: 36921255 DOI: 10.1021/acs.jproteome.3c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Method optimization is crucial for successful mass spectrometry (MS) analysis. However, extensive method assessments, altering various parameters individually, are rarely performed due to practical limitations regarding time and sample quantity. To maximize sample space for optimization while maintaining reasonable instrumentation requirements, a definitive screening design (DSD) is leveraged for systematic optimization of data-independent acquisition (DIA) parameters to maximize crustacean neuropeptide identifications. While DSDs require several injections, a library-free methodology enables surrogate sample usage for comprehensive optimization of MS parameters to assess biomolecules from limited samples. We identified several parameters contributing significant first- or second-order effects to method performance, and the DSD model predicted ideal values to implement. These increased reproducibility and detection capabilities enabled the identification of 461 peptides, compared to 375 and 262 peptides identified through data-dependent acquisition (DDA) and a published DIA method for crustacean neuropeptides, respectively. Herein, we demonstrate a DSD optimization workflow, using standard material, not reliant on spectral libraries for the analysis of any low abundance molecules from previous samples of limited availability. This extends the DIA method to low abundance isoforms dysregulated or only detectable in disease samples, thus improving characterization of previously inaccessible biomolecules, such as neuropeptides. Data are available via ProteomeXchange with identifier PXD038520.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Austin V Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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30
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Integration of a hybrid scan approach and in-house high-resolution MS2 spectral database for charactering the multicomponents of Xuebijing Injection. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2022.104519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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31
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Qian L, Zhu J, Xue Z, Gong T, Xiang N, Yue L, Cai X, Gong W, Wang J, Sun R, Jiang W, Ge W, Wang H, Zheng Z, Wu Q, Zhu Y, Guo T. Resistance prediction in high-grade serous ovarian carcinoma with neoadjuvant chemotherapy using data-independent acquisition proteomics and an ovary-specific spectral library. Mol Oncol 2023. [PMID: 36855266 PMCID: PMC10399723 DOI: 10.1002/1878-0261.13410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/25/2022] [Accepted: 02/27/2023] [Indexed: 03/02/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most common subtype of ovarian cancer with 5-year survival rates below 40%. Neoadjuvant chemotherapy (NACT) followed by interval debulking surgery (IDS) is recommended for patients with advanced-stage HGSOC unsuitable for primary debulking surgery (PDS). However, about 40% of patients receiving this treatment exhibited chemoresistance of uncertain molecular mechanisms and predictability. Here, we built a high-quality ovary-specific spectral library containing 130 735 peptides and 10 696 proteins on Orbitrap instruments. Compared to a published DIA pan-human spectral library (DPHL), this spectral library provides 10% more ovary-specific and 3% more ovary-enriched proteins. This library was then applied to analyze data-independent acquisition (DIA) data of tissue samples from an HGSOC cohort treated with NACT, leading to 10 070 quantified proteins, which is 9.73% more than that with DPHL. We further established a six-protein classifier by parallel reaction monitoring (PRM) to effectively predict the resistance to additional chemotherapy after IDS (Log-rank test, P = 0.002). The classifier was validated with 57 patients from an independent clinical center (P = 0.014). Thus, we have developed an ovary-specific spectral library for targeted proteome analysis, and propose a six-protein classifier that could potentially predict chemoresistance in HGSOC patients after NACT-IDS treatment.
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Affiliation(s)
- Liujia Qian
- School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jianqing Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Zhangzhi Xue
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tingting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Nan Xiang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Liang Yue
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xue Cai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Wangang Gong
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Junjian Wang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Rui Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Wenhao Jiang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., China
| | - He Wang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Zhiguo Zheng
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Qijun Wu
- Department of Clinical Epidemiology, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tiannan Guo
- School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
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32
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Zhao J, Yang Y, Xu H, Zheng J, Shen C, Chen T, Wang T, Wang B, Yi J, Zhao D, Wu E, Qin Q, Xia L, Qiao L. Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota. NPJ Biofilms Microbiomes 2023; 9:4. [PMID: 36693863 PMCID: PMC9873935 DOI: 10.1038/s41522-023-00373-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.
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Affiliation(s)
- Jinzhi Zhao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Yi Yang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 311200, Hangzhou, China
| | - Hua Xu
- Department of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Jianxujie Zheng
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Chengpin Shen
- Shanghai Omicsolution Co., Ltd, 201100, Shanghai, China
| | - Tian Chen
- Changhai Hospital, The Naval Military Medical University, 200433, Shanghai, China
| | - Tao Wang
- Department of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Bing Wang
- College of Food Science and Technology, Shanghai Ocean University, 201306, Shanghai, China
| | - Jia Yi
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Dan Zhao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Enhui Wu
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Qin Qin
- Changhai Hospital, The Naval Military Medical University, 200433, Shanghai, China.
| | - Li Xia
- Department of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China.
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33
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Fu J, Yang Q, Luo Y, Zhang S, Tang J, Zhang Y, Zhang H, Xu H, Zhu F. Label-free proteome quantification and evaluation. Brief Bioinform 2023; 24:6833644. [PMID: 36403090 DOI: 10.1093/bib/bbac477] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/24/2022] [Accepted: 10/08/2022] [Indexed: 11/21/2022] Open
Abstract
The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on >3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingxia Yang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Song Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Tang
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hanxiang Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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34
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Casavant EP, Liang J, Sankhe S, Mathews WR, Anania VG. Using SILAC to Develop Quantitative Data-Independent Acquisition (DIA) Proteomic Methods. Methods Mol Biol 2023; 2603:245-257. [PMID: 36370285 DOI: 10.1007/978-1-0716-2863-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Proteins are integral to biological systems and functions. Identifying and quantifying proteins can therefore offer systems-wide insights into protein-protein interactions, cellular signaling, and biological pathway activity. The use of quantitative proteomics has become a method of choice for identifying and quantifying proteins in complex matrices. Proteomics allows researchers to survey hundreds to thousands of proteins in a less biased manner than classical antibody-based protein capture strategies. Typically, discovery approaches have used data-dependent acquisition (DDA) methods, but this approach suffers from stochasticity that compromises quantitation. Recent developments in data-independent acquisition (DIA) proteomics workflows enable proteomic profiling of thousands of samples with increased peak picking consistency making it an excellent candidate for discovering and assessing biomarkers in clinical samples. However, quantitation of peptides from DIA datasets is computationally intensive, and guidelines on how to establish DIA methods are lacking. Method development and optimization require novel tools to visualize and filter DIA datasets appropriately. Here, a protocol and novel script workflow for the optimization of quantitative DIA methods using stable isotope labeling of amino acids in culture (SILAC) are presented. This protocol includes steps for cell growth and labeling, peptide digestion and preparation, and optimization of quantitative DIA methods. In addition, important steps for (1) computational analysis to identify and quantify peptides, (2) data visualizations to identify the linear abundance ranges for all peptides in the sample, and (3) descriptions of how to find high confidence quantitation abundance thresholds are described herein.
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35
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Bersching K, Michna T, Tenzer S, Jacob S. Data-Independent Acquisition (DIA) Is Superior for High Precision Phospho-Peptide Quantification in Magnaporthe oryzae. J Fungi (Basel) 2022; 9:jof9010063. [PMID: 36675884 PMCID: PMC9863866 DOI: 10.3390/jof9010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
The dynamic interplay of signaling networks in most major cellular processes is characterized by the orchestration of reversible protein phosphorylation. Consequently, analytic methods such as quantitative phospho-peptidomics have been pushed forward from a highly specialized edge-technique to a powerful and versatile platform for comprehensively analyzing the phosphorylation profile of living organisms. Despite enormous progress in instrumentation and bioinformatics, a high number of missing values caused by the experimental procedure remains a major problem, due to either a random phospho-peptide enrichment selectivity or borderline signal intensities, which both cause the exclusion for fragmentation using the commonly applied data dependent acquisition (DDA) mode. Consequently, an incomplete dataset reduces confidence in the subsequent statistical bioinformatic processing. Here, we successfully applied data independent acquisition (DIA) by using the filamentous fungus Magnaporthe oryzae as a model organism, and could prove that while maintaining data quality (such as phosphosite and peptide sequence confidence), the data completeness increases dramatically. Since the method presented here reduces the LC-MS/MS analysis from 3 h to 1 h and increases the number of phosphosites identified up to 10-fold in contrast to published studies in Magnaporthe oryzae, we provide a refined methodology and a sophisticated resource for investigation of signaling processes in filamentous fungi.
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Affiliation(s)
- Katharina Bersching
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55131 Mainz, Germany
| | - Thomas Michna
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
- Helmholtz-Institute for Translational Oncology Mainz (HI-TRON), 55131 Mainz, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Jacob
- Institute of Biotechnology and Drug Research gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55131 Mainz, Germany
- Correspondence:
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36
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Proteomic overview of hepatocellular carcinoma cell lines and generation of the spectral library. Sci Data 2022; 9:732. [PMID: 36446815 PMCID: PMC9708666 DOI: 10.1038/s41597-022-01845-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
Cell lines are extensively used tools, therefore a comprehensive proteomic overview of hepatocellular carcinoma (HCC) cell lines and an extensive spectral library for data independent acquisition (DIA) quantification are necessary. Here, we present the proteome of nine commonly used HCC cell lines covering 9,208 protein groups, and the HCC spectral library containing 253,921 precursors, 168,811 peptides and 10,098 protein groups. The proteomic overview reveals the heterogeneity between different cell lines, and the similarity in proliferation and metastasis characteristics and drug targets-expression with tumour tissues. The HCC spectral library generating consumed 108 hours' runtime for data dependent acquisition (DDA) of 48 runs, 24 hours' runtime for database searching by MaxQuant version 2.0.3.0, and 1 hour' runtime for processing by SpectronautTM version 15.2. The HCC spectral library supports quantification of 7,637 protein groups of triples 2-hour DIA analysis of HepG2 and discovering biological alteration. This study provides valuable resources for HCC cell lines and efficient DIA quantification on LC-Orbitrap platform, further help to explore the molecular mechanism and candidate therapeutic targets.
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37
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Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs. PLoS One 2022; 17:e0276401. [PMID: 36269744 PMCID: PMC9586388 DOI: 10.1371/journal.pone.0276401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
In bottom-up proteomics, proteins are enzymatically digested into peptides before measurement with mass spectrometry. The relationship between proteins and their corresponding peptides can be represented by bipartite graphs. We conduct a comprehensive analysis of bipartite graphs using quantified peptides from measured data sets as well as theoretical peptides from an in silico digestion of the corresponding complete taxonomic protein sequence databases. The aim of this study is to characterize and structure the different types of graphs that occur and to compare them between data sets. We observed a large influence of the accepted minimum peptide length during in silico digestion. When changing from theoretical peptides to measured ones, the graph structures are subject to two opposite effects. On the one hand, the graphs based on measured peptides are on average smaller and less complex compared to graphs using theoretical peptides. On the other hand, the proportion of protein nodes without unique peptides, which are a complicated case for protein inference and quantification, is considerably larger for measured data. Additionally, the proportion of graphs containing at least one protein node without unique peptides rises when going from database to quantitative level. The fraction of shared peptides and proteins without unique peptides as well as the complexity and size of the graphs highly depends on the data set and organism. Large differences between the structures of bipartite peptide-protein graphs have been observed between database and quantitative level as well as between analyzed species. In the analyzed measured data sets, the proportion of protein nodes without unique peptides ranged from 6.4% to 55.0%. This highlights the need for novel methods that can quantify proteins without unique peptides. The knowledge about the structure of the bipartite peptide-protein graphs gained in this study will be useful for the development of such algorithms.
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38
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Gagné D, Shajari E, Thibault MP, Noël JF, Boisvert FM, Babakissa C, Levy E, Gagnon H, Brunet MA, Grynspan D, Ferretti E, Bertelle V, Beaulieu JF. Proteomics Profiling of Stool Samples from Preterm Neonates with SWATH/DIA Mass Spectrometry for Predicting Necrotizing Enterocolitis. Int J Mol Sci 2022; 23:ijms231911601. [PMID: 36232903 PMCID: PMC9569884 DOI: 10.3390/ijms231911601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is a life-threatening condition for premature infants in neonatal intensive care units. Finding indicators that can predict NEC development before symptoms appear would provide more time to apply targeted interventions. In this study, stools from 132 very-low-birth-weight (VLBW) infants were collected daily in the context of a multi-center prospective study aimed at investigating the potential of fecal biomarkers for NEC prediction using proteomics technology. Eight of the VLBW infants received a stage-3 NEC diagnosis. Stools collected from the NEC infants up to 10 days before their diagnosis were available for seven of them. Their samples were matched with those from seven pairs of non-NEC controls. The samples were processed for liquid chromatography-tandem mass spectrometry analysis using SWATH/DIA acquisition and cross-compatible proteomic software to perform label-free quantification. ROC curve and principal component analyses were used to explore discriminating information and to evaluate candidate protein markers. A series of 36 proteins showed the most efficient capacity with a signature that predicted all seven NEC infants at least a week in advance. Overall, our study demonstrates that multiplexed proteomic signature detection constitutes a promising approach for the early detection of NEC development in premature infants.
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Affiliation(s)
- David Gagné
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Elmira Shajari
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Marie-Pier Thibault
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Jean-François Noël
- PhenoSwitch Bioscience Inc., 975 Rue Léon-Trépanier, Sherbrooke, QC J1G 5J6, Canada
| | - François-Michel Boisvert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Corentin Babakissa
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Emile Levy
- Research Center, Centre Hospitalier Universitaire Ste-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Hugo Gagnon
- PhenoSwitch Bioscience Inc., 975 Rue Léon-Trépanier, Sherbrooke, QC J1G 5J6, Canada
| | - Marie A. Brunet
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - David Grynspan
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Colombia, Vancouver, BC V6T 2B5, Canada
| | - Emanuela Ferretti
- Division of Neonatology, Department of Pediatrics, Children’s Hospital of Eastern Ontario (CHEO) and CHEO Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Valérie Bertelle
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Division of Neonatology, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Jean-François Beaulieu
- Laboratory of Intestinal Physiopathology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Correspondence:
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Uszkoreit J, Barkovits K, Pacharra S, Pfeiffer K, Steinbach S, Marcus K, Eisenacher M. Dataset containing physiological amounts of spike-in proteins into murine C2C12 background as a ground truth quantitative LC-MS/MS reference. Data Brief 2022; 43:108435. [PMID: 35845101 PMCID: PMC9283871 DOI: 10.1016/j.dib.2022.108435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 10/24/2022] Open
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40
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Bacala R, Hatcher DW, Perreault H, Fu BX. Challenges and opportunities for proteomics and the improvement of bread wheat quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153743. [PMID: 35749977 DOI: 10.1016/j.jplph.2022.153743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Wheat remains a critical global food source, pressured by climate change and the need to maximize yield, improve processing and nutritional quality and ensure safety. An enormous amount of research has been conducted to understand gluten protein composition and structure in relation to end-use quality, yet progress has become stagnant. This is mainly due to the need and inability to biochemically characterize the intact functional glutenin polymer in order to correlate to quality, necessitating reduction to monomeric subunits and a loss of contextual information. While some individual gluten proteins might have a positive or negative influence on gluten quality, it is the sum total of these proteins, their relative and absolute expression, their sub-cellular trafficking, the amount and size of glutenin polymers, and ratios between gluten protein classes that define viscoelasticity of gluten. The sub-cellular trafficking of gluten proteins during seed maturation is still not completely clear and there is evidence of dual pathways and therefore different destinations for proteins, either constitutively or temporally. The trafficking of proteins is also unclear in endosperm cells as they undergo programmed cell death; Golgi disappear around 12 DPA but protein filling continues at least to 25 DPA. Modulation of the timing of cellular events will invariably affect protein deposition and therefore gluten strength and function. Existing and emerging proteomics technologies such as proteoform profiling and top-down proteomics offer new tools to study gluten protein composition as a whole system and identify compositional patterns that can modify gluten structure with improved functionality.
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Affiliation(s)
- Ray Bacala
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Dave W Hatcher
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada
| | - Héléne Perreault
- University of Manitoba, Department of Chemistry, 144 Dysart Road, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Bin Xiao Fu
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, Manitoba, R3C 3G8, Canada; Department of Food and Human Nutritional Sciences, 209 - 35 Chancellor's Circle, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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41
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Wang Y, Lih TSM, Chen L, Xu Y, Kuczler MD, Cao L, Pienta KJ, Amend SR, Zhang H. Optimized data-independent acquisition approach for proteomic analysis at single-cell level. Clin Proteomics 2022; 19:24. [PMID: 35810282 PMCID: PMC9270744 DOI: 10.1186/s12014-022-09359-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/26/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Single-cell proteomic analysis provides valuable insights into cellular heterogeneity allowing the characterization of the cellular microenvironment which is difficult to accomplish in bulk proteomic analysis. Currently, single-cell proteomic studies utilize data-dependent acquisition (DDA) mass spectrometry (MS) coupled with a TMT labelled carrier channel. Due to the extremely imbalanced MS signals among the carrier channel and other TMT reporter ions, the quantification is compromised. Thus, data-independent acquisition (DIA)-MS should be considered as an alternative approach towards single-cell proteomic study since it generates reproducible quantitative data. However, there are limited reports on the optimal workflow for DIA-MS-based single-cell analysis. METHODS We report an optimized DIA workflow for single-cell proteomics using Orbitrap Lumos Tribrid instrument. We utilized a breast cancer cell line (MDA-MB-231) and induced drug resistant polyaneuploid cancer cells (PACCs) to evaluate our established workflow. RESULTS We found that a short LC gradient was preferable for peptides extracted from single cell level with less than 2 ng sample amount. The total number of co-searching peptide precursors was also critical for protein and peptide identifications at nano- and sub-nano-gram levels. Post-translationally modified peptides could be identified from a nano-gram level of peptides. Using the optimized workflow, up to 1500 protein groups were identified from a single PACC corresponding to 0.2 ng of peptides. Furthermore, about 200 peptides with phosphorylation, acetylation, and ubiquitination were identified from global DIA analysis of 100 cisplatin resistant PACCs (20 ng). Finally, we used this optimized DIA approach to compare the whole proteome of MDA-MB-231 parental cells and induced PACCs at a single-cell level. We found the single-cell level comparison could reflect real protein expression changes and identify the protein copy number. CONCLUSIONS Our results demonstrate that the optimized DIA pipeline can serve as a reliable quantitative tool for single-cell as well as sub-nano-gram proteomic analysis.
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Affiliation(s)
- Yuefan Wang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | | | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Yuanwei Xu
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Morgan D Kuczler
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Liwei Cao
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kenneth J Pienta
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Sarah R Amend
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA.
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42
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Zeng X, Lan Y, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Peng T, Long F. Advances in phosphoproteomics and its application to COPD. Expert Rev Proteomics 2022; 19:311-324. [PMID: 36730079 DOI: 10.1080/14789450.2023.2176756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities. AREAS COVERED In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease. EXPERT OPINION The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.
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Affiliation(s)
- Xiaoyin Zeng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yanting Lan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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43
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De La Toba EA, Bell SE, Romanova EV, Sweedler JV. Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:83-106. [PMID: 35324254 DOI: 10.1146/annurev-anchem-061020-022048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.
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Affiliation(s)
- Eduardo A De La Toba
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sara E Bell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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44
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Mi Y, Hu W, Li W, Wan S, Xu X, Liu M, Wang H, Mei Q, Chen Q, Yang Y, Chen B, Jiang M, Li X, Yang W, Guo D. Systematic Qualitative and Quantitative Analyses of Wenxin Granule via Ultra-High Performance Liquid Chromatography Coupled with Ion Mobility Quadrupole Time-of-Flight Mass Spectrometry and Triple Quadrupole–Linear Ion Trap Mass Spectrometry. Molecules 2022; 27:molecules27113647. [PMID: 35684583 PMCID: PMC9181919 DOI: 10.3390/molecules27113647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022] Open
Abstract
Wenxin granule (WXG) is a popular traditional Chinese medicine (TCM) preparation for the treatment of arrhythmia disease. Potent analytical technologies are needed to elucidate its chemical composition and assess the quality differences among multibatch samples. In this work, both a multicomponent characterization and quantitative assay of WXG were conducted using two liquid chromatography–mass spectrometry (LC-MS) approaches. An ultra-high performance liquid chromatography–ion mobility quadrupole time-of-flight mass spectrometry (UHPLC/IM-QTOF-MS) approach combined with intelligent peak annotation workflows was developed to characterize the multicomponents of WXG. A hybrid scan approach enabling alternative data-independent and data-dependent acquisitions was established. We characterized 205 components, including 92 ginsenosides, 53 steroidal saponins, 14 alkaloids, and 46 others. Moreover, an optimized scheduled multiple reaction monitoring (sMRM) method was elaborated, targeting 24 compounds of WXG via ultra-high performance liquid chromatography–triple quadrupole linear ion trap mass spectrometry (UHPLC/QTrap-MS), which was validated based on its selectivity, precision, stability, repeatability, linearity, sensitivity, recovery, and matrix effect. By applying this method to 27 batches of WXG samples, the content variations of multiple markers from Notoginseng Radix et Rhizoma (21) and Codonopsis Radix (3) were depicted. Conclusively, we achieved the comprehensive multicomponent characterization and holistic quality assessment of WXG by targeting the non-volatile components.
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Affiliation(s)
- Yueguang Mi
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Wandi Hu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Weiwei Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Shiyu Wan
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Xiaoyan Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Meiyu Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Hongda Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Quanxi Mei
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Yang Yang
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China; (S.W.); (Q.M.); (Q.C.); (Y.Y.)
| | - Boxue Chen
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Meiting Jiang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Xue Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
| | - Wenzhi Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
- Correspondence: ; Tel.: +86-022-5979-1833
| | - Dean Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai, Tianjin 301617, China; (Y.M.); (W.H.); (W.L.); (X.X.); (M.L.); (H.W.); (B.C.); (M.J.); (X.L.); (D.G.)
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
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Fröhlich K, Brombacher E, Fahrner M, Vogele D, Kook L, Pinter N, Bronsert P, Timme-Bronsert S, Schmidt A, Bärenfaller K, Kreutz C, Schilling O. Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. Nat Commun 2022; 13:2622. [PMID: 35551187 PMCID: PMC9098472 DOI: 10.1038/s41467-022-30094-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/14/2022] [Indexed: 12/25/2022] Open
Abstract
Numerous software tools exist for data-independent acquisition (DIA) analysis of clinical samples, necessitating their comprehensive benchmarking. We present a benchmark dataset comprising real-world inter-patient heterogeneity, which we use for in-depth benchmarking of DIA data analysis workflows for clinical settings. Combining spectral libraries, DIA software, sparsity reduction, normalization, and statistical tests results in 1428 distinct data analysis workflows, which we evaluate based on their ability to correctly identify differentially abundant proteins. From our dataset, we derive bootstrap datasets of varying sample sizes and use the whole range of bootstrap datasets to robustly evaluate each workflow. We find that all DIA software suites benefit from using a gas-phase fractionated spectral library, irrespective of the library refinement used. Gas-phase fractionation-based libraries perform best against two out of three reference protein lists. Among all investigated statistical tests non-parametric permutation-based statistical tests consistently perform best. Data independent acquisition (DIA) has been gaining momentum in clinical proteomics. Here, the authors create a benchmark dataset comprising inter-patient heterogeneity to compare popular DIA data analysis workflows for identifying differentially abundant proteins.
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Affiliation(s)
- Klemens Fröhlich
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany.,Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg im Breisgau, Germany
| | - Eva Brombacher
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg im Breisgau, Germany.,Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg im Breisgau, Germany.,Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg im Breisgau, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany.,Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg im Breisgau, Germany
| | - Daniel Vogele
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany.,Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Lucas Kook
- Epidemiology, Biostatistics & Prevention Institute, University of Zurich, Zurich, Switzerland.,Institute for Data Analysis and Process Design, Zurich University of Applied Sciences, Winterthur, Switzerland
| | - Niko Pinter
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Tumorbank Comprehensive Cancer Center Freiburg, Medical Center University of Freiburg, Freiburg im Breisgau, Germany
| | - Sylvia Timme-Bronsert
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany.,Tumorbank Comprehensive Cancer Center Freiburg, Medical Center University of Freiburg, Freiburg im Breisgau, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Katja Bärenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, and Swiss Institute of Bioinformatics (SIB), Wolfgang, Switzerland
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg im Breisgau, Germany.,Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg im Breisgau, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany. .,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany.
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46
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Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi. Curr Issues Mol Biol 2022; 44:2069-2088. [PMID: 35678669 PMCID: PMC9164042 DOI: 10.3390/cimb44050140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 11/17/2022] Open
Abstract
An important step in the proteomic analysis of missing proteins is the use of a wide range of tissues, optimal extraction, and the processing of protein material in order to ensure the highest sensitivity in downstream protein detection. This work describes a purification protocol for identifying low-abundance proteins in human chorionic villi using the proposed “1DE-gel concentration” method. This involves the removal of SDS in a short electrophoresis run in a stacking gel without protein separation. Following the in-gel digestion of the obtained holistic single protein band, we used the peptide mixture for further LC–MS/MS analysis. Statistically significant results were derived from six datasets, containing three treatments, each from two tissue sources (elective or missed abortions). The 1DE-gel concentration increased the coverage of the chorionic villus proteome. Our approach allowed the identification of 15 low-abundance proteins, of which some had not been previously detected via the mass spectrometry of trophoblasts. In the post hoc data analysis, we found a dubious or uncertain protein (PSG7) encoded on human chromosome 19 according to neXtProt. A proteomic sample preparation workflow with the 1DE-gel concentration can be used as a prospective tool for uncovering the low-abundance part of the human proteome.
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47
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Jiang N, Gao Y, Xu J, Luo F, Zhang X, Chen R. A data-independent acquisition (DIA)-based quantification workflow for proteome analysis of 5000 cells. J Pharm Biomed Anal 2022; 216:114795. [PMID: 35489320 DOI: 10.1016/j.jpba.2022.114795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022]
Abstract
Data independent acquisition (DIA) has emerged as a powerful proteomic technique with exceptional reproducibility and throughput, and has been widely applied to clinical sample analysis. DIA approaches normally rely on project-specific spectral libraries generated by data dependent acquisition (DDA), requiring extensive off-line fractionation and large amounts of input material. In this study, we aimed to explore the utility of DIA for the analysis of samples with limited quantities. We employed three software tools (DIA-NN, Spectronaut, and EncyclopeDIA) for data analysis and generated three types of libraries, including an experiment-specific library built by DDA analysis of off-line fractions, a FASTA sequence database, and a library generated by gas-phase fractionation (GPF), resulting in eight analysis pipelines. Then we systematically compared the performance of the eight strategies by analyzing the DIA data from HEK293T cell tryptic peptides with sample loads of 500 ng, 100 ng, 20 ng, and 4 ng. The results showed that DIA-NN with GPF-based libraries outperformed the others in protein identification and retention time calibration. Next, we further evaluated the optimized workflow by analyzing the proteome alteration in 5000 peripheral blood mononuclear cells (PBMCs) induced by lipopolysaccharide (LPS) stimulation. As a result, 3179 protein groups were quantified, and functional analysis revealed activation of multiple signaling pathways, e. g., endocytosis, NF-kappa B signaling, and T cell receptor signaling. The results showed the practicability of using DIA for scarce samples, and the established workflow of PBMC analysis could be easily adapted for biomarker discovery, immune status evaluation, and drug response monitoring, especially for diseases involved with dysfunction of the immune system.
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Affiliation(s)
- Na Jiang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jia Xu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Fengting Luo
- Department of Clinical Laboratory, Tianjin Hospital, Tianjin 300142, China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
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48
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Quantitative Proteomics Reveals Metabolic Reprogramming in Host Cells Induced by Trophozoites and Intermediate Subunit of Gal/GalNAc Lectins from Entamoeba histolytica. mSystems 2022; 7:e0135321. [PMID: 35343800 PMCID: PMC9040881 DOI: 10.1128/msystems.01353-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Entamoeba histolytica is an intestinal protozoan parasite with remarkable ability to kill and phagocytose host cells, causing amoebic colitis and extraintestinal abscesses. The intermediate subunit (Igl) of galactose (Gal)- and N-acetyl-d-galactosamine (GalNAc)-specific lectins is considered an important surface antigen involved in the pathogenesis of E. histolytica. Here, we applied mass spectrometry-based quantitative proteomics technology to analyze the protein expression profile changes occurring in host Caco2 cells incubated with E. histolytica trophozoites or stimulated by purified native Igl protein. The expression levels of 1,490 and 489 proteins were significantly altered in the E. histolytica-treated and Igl-treated groups, respectively, among 6,875 proteins totally identified. Intriguingly, central carbon metabolism of host cells was suppressed in both E. histolytica-treated and Igl-treated groups, with evidence of decreased expression levels of several key enzymes, including pyruvate kinase muscle type 2, presenting a Warburg-like effect in host cells. Besides, Igl had potential physical interactions with central carbon metabolism enzymes and the proteolytic degradation family members proteasome subunit alpha and beta, which may be responsible for the degradation of key enzymes in carbon metabolism. These results provided a novel perspective on the pathogenic mechanism of E. histolytica and compelling evidence supporting the important role of Igl in the virulence of E. histolytica. IMPORTANCE Metabolic reprogramming is considered a hallmark of some infectious diseases. However, in amoebiasis, a neglected tropical disease caused by protozoan parasite E. histolytica, metabolic changes in host cells have yet to be proven. In this study, advanced data-independent acquisition mass spectrometry-based quantitative proteomics was applied to investigate the overall host cellular metabolic changes as high-throughput proteomics could measure molecular changes in a cell or tissue with high efficiency. Enrichment analysis of differentially expressed proteins showed biological processes and cellular pathways related to amoeba infection and Igl cytotoxicity. Specifically, central carbon metabolism of host cells was dramatically suppressed in both E. histolytica-treated and Igl-treated groups, indicating the occurrence of a Warburg-like effect induced by trophozoites or Igl from E. histolytica. Distinct differences in ubiquitin-mediated proteolysis, rapamycin (mTOR) signaling pathway, autophagy, endocytosis, and tight junctions provided novel perspectives on the pathogenic mechanism of E. histolytica.
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Siddiqui G, De Paoli A, MacRaild CA, Sexton AE, Boulet C, Shah AD, Batty MB, Schittenhelm RB, Carvalho TG, Creek DJ. A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome. Gigascience 2022; 11:6543637. [PMID: 35254426 PMCID: PMC8900498 DOI: 10.1093/gigascience/giac008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/24/2021] [Accepted: 01/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background Plasmodium falciparum causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an important research focus. In recent years, mass spectrometry–based proteomics using data-dependent acquisition has been extensively used to understand the biochemical processes within the parasite. However, data-dependent acquisition is problematic for the detection of low-abundance proteins and proteome coverage and has poor run-to-run reproducibility. Results Here, we present a comprehensive P. falciparum–infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 P. falciparum and 1,617 RBC proteins using a data-independent acquisition mass spectrometric approach. The spectral library includes proteins expressed in the 3 morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs. This spectral library contains 87% of all P. falciparum proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The P. falciparum spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterize the 3 distinct asexual parasite stages in RBCs, and compared artemisinin-resistant (Cam3.IIR539T) and artemisinin-sensitive (Cam3.IIrev) parasites. Conclusion A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of P. falciparum malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms, and vaccine candidate discovery for malaria.
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Affiliation(s)
- Ghizal Siddiqui
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Amanda De Paoli
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Christopher A MacRaild
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Anna E Sexton
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Coralie Boulet
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Anup D Shah
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mitchell B Batty
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Teresa G Carvalho
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Darren J Creek
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
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Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
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