1
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Meldrum KL, Swansiger AK, Daniels MM, Hale WA, Kirmiz Cody C, Qiu X, Knierman M, Sausen J, Prell JS. Gábor Transform-Based Signal Isolation, Rapid Deconvolution, and Quantitation of Intact Protein Ions with Mass Spectrometry. Anal Chem 2024. [PMID: 38788216 DOI: 10.1021/acs.analchem.4c00978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
High-resolution mass spectrometry (HRMS) is a powerful technique for the characterization and quantitation of complex biological mixtures, with several applications including clinical monitoring and tissue imaging. However, these medical and pharmaceutical applications are pushing the analytical limits of modern HRMS techniques, requiring either further development in instrumentation or data processing methods. Here, we demonstrate new developments in the interactive Fourier-transform analysis for mass spectrometry (iFAMS) software including the first application of Gábor transform (GT) to protein quantitation. Newly added automation tools detect signals from minimal user input and apply thresholds for signal selection, deconvolution, and baseline correction to improve the objectivity and reproducibility of deconvolution. Additional tools were added to improve the deconvolution of highly complex or congested mass spectra and are demonstrated here for the first time. The "Gábor Slicer" enables the user to explore trends in the Gábor spectrogram with instantaneous ion mass estimates accurate to 10 Da. The charge adjuster allows for easy visual confirmation of accurate charge state assignments and quick adjustment if necessary. Deconvolution refinement utilizes a second GT of isotopically resolved data to remove common deconvolution artifacts. To assess the quality of deconvolution from iFAMS, several comparisons are made to deconvolutions using other algorithms such as UniDec and an implementation of MaxEnt in Agilent MassHunter BioConfirm. Lastly, the newly added batch processing and quantitation capabilities of iFAMS are demonstrated and compared to a common extracted ion chromatogram approach.
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Affiliation(s)
- Kayd L Meldrum
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Andrew K Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Meghan M Daniels
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Wendi A Hale
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Crystal Kirmiz Cody
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Xi Qiu
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Michael Knierman
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - John Sausen
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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2
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Naryzhny S. Puzzle of Proteoform Variety-Where Is a Key? Proteomes 2024; 12:15. [PMID: 38804277 PMCID: PMC11130821 DOI: 10.3390/proteomes12020015] [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: 01/31/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.
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Affiliation(s)
- Stanislav Naryzhny
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad Region, Gatchina 188300, Russia
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3
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Carr AV, Bollis NE, Pavek JG, Shortreed MR, Smith LM. Spectral averaging with outlier rejection algorithms to increase identifications in top-down proteomics. Proteomics 2024; 24:e2300234. [PMID: 38487981 DOI: 10.1002/pmic.202300234] [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: 05/31/2023] [Revised: 02/15/2024] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
The identification of proteoforms by top-down proteomics requires both high quality fragmentation spectra and the neutral mass of the proteoform from which the fragments derive. Intact proteoform spectra can be highly complex and may include multiple overlapping proteoforms, as well as many isotopic peaks and charge states. The resulting lower signal-to-noise ratios for intact proteins complicates downstream analyses such as deconvolution. Averaging multiple scans is a common way to improve signal-to-noise, but mass spectrometry data contains artifacts unique to it that can degrade the quality of an averaged spectra. To overcome these limitations and increase signal-to-noise, we have implemented outlier rejection algorithms to remove outlier measurements efficiently and robustly in a set of MS1 scans prior to averaging. We have implemented averaging with rejection algorithms in the open-source, freely available, proteomics search engine MetaMorpheus. Herein, we report the application of the averaging with rejection algorithms to direct injection and online liquid chromatography mass spectrometry data. Averaging with rejection algorithms demonstrated a 45% increase in the number of proteoforms detected in Jurkat T cell lysate. We show that the increase is due to improved spectral quality, particularly in regions surrounding isotopic envelopes.
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Affiliation(s)
- Austin V Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicholas E Bollis
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John G Pavek
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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4
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Banerjee S, Hatimuria M, Sarkar K, Das J, Pabbathi A, Sil PC. Recent Contributions of Mass Spectrometry-Based "Omics" in the Studies of Breast Cancer. Chem Res Toxicol 2024; 37:137-180. [PMID: 38011513 DOI: 10.1021/acs.chemrestox.3c00223] [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: 11/29/2023]
Abstract
Breast cancer (BC) is one of the most heterogeneous groups of cancer. As every biotype of BC is unique and presents a particular "omic" signature, they are increasingly characterized nowadays with novel mass spectrometry (MS) strategies. BC therapeutic approaches are primarily based on the two features of human epidermal growth factor receptor 2 (HER2) and estrogen receptor (ER) positivity. Various strategic MS implementations are reported in studies of BC also involving data independent acquisitions (DIAs) of MS which report novel differential proteomic, lipidomic, proteogenomic, phosphoproteomic, and metabolomic characterizations associated with the disease and its therapeutics. Recently many "omic" studies have aimed to identify distinct subsidiary biotypes for diagnosis, prognosis, and targets of treatment. Along with these, drug-induced-resistance phenotypes are characterized by "omic" changes. These identifying aspects of the disease may influence treatment outcomes in the near future. Drug quantifications and characterizations are also done regularly and have implications in therapeutic monitoring and in drug efficacy assessments. We report these studies, mentioning their implications toward the understanding of BC. We briefly provide the MS instrumentation principles that are adopted in such studies as an overview with a brief outlook on DIA-MS strategies. In all of these, we have chosen a model cancer for its revelations through MS-based "omics".
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Affiliation(s)
- Subhrajit Banerjee
- Department of Physiology, Surendranath College, University of Calcutta, Kolkata 700009, India
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Madushmita Hatimuria
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Kasturi Sarkar
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Joydeep Das
- Department of Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram, India
| | - Ashok Pabbathi
- Department of Industrial Chemistry, School of Physical Sciences, Mizoram University, Aizawl 796004, Mizoram India
| | - Parames C Sil
- Department of Molecular Medicine Bose Institute, Kolkata 700054, India
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5
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Dowling P, Trollet C, Negroni E, Swandulla D, Ohlendieck K. How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes 2024; 12:4. [PMID: 38250815 PMCID: PMC10801633 DOI: 10.3390/proteomes12010004] [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: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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6
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Di Tucci C, Muzii L. Chronic Pelvic Pain, Vulvar Pain Disorders, and Proteomics Profiles: New Discoveries, New Hopes. Biomedicines 2023; 12:1. [PMID: 38275362 PMCID: PMC10813718 DOI: 10.3390/biomedicines12010001] [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: 11/08/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Chronic pelvic pain (CPP) is generally defined as non-cyclic pain perceived in the pelvic area that has persisted from three to six months or longer and is unrelated to pregnancy. The etiology of CPP is complex, multifactorial, with heterogeneous presentation, and includes several diseases such as endometriosis, adenomyosis, and interstitial cystitis/bladder pain syndrome. It may also be associated with sexual dysfunction, musculoskeletal disorders, and comorbid psychiatric symptoms. Vulvar pain disorders (VPDs) are typically categorized separately from chronic pelvic pain; among all VPDs, vulvodynia is a chronic vulvar pain of unknown etiology, lasting at least 3 months and that might be associated with other potentially linked factors. Proteomics represents a useful approach to study the proteome profiles of clinical samples. In this review, we have considered a selection of articles that have analyzed the protein abundance and novel protein species from various biological samples, including eutopic/ectopic endometrium, urine, serum, follicular, peritoneal fluid, and cervical mucus, potentially involved in the pathogenesis and progression of CPP and VPDs. These findings could represent valuable targets for paving the way for the differential diagnosis and therapeutic management of CPP and VDPs, thereby optimizing both the prevention and treatment of these conditions.
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Affiliation(s)
- Chiara Di Tucci
- Department of Obstetrics and Gynecology, “Sapienza” University, 00185 Rome, Italy;
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7
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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8
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Chen W, Ding Z, Zang Y, Liu X. Characterization of Proteoform Post-Translational Modifications by Top-Down and Bottom-Up Mass Spectrometry in Conjunction with Annotations. J Proteome Res 2023; 22:3178-3189. [PMID: 37728997 PMCID: PMC10563160 DOI: 10.1021/acs.jproteome.3c00207] [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: 04/07/2023] [Indexed: 09/22/2023]
Abstract
Many proteoforms can be produced from a gene due to genetic mutations, alternative splicing, post-translational modifications (PTMs), and other variations. PTMs in proteoforms play critical roles in cell signaling, protein degradation, and other biological processes. Mass spectrometry (MS) is the primary technique for investigating PTMs in proteoforms, and two alternative MS approaches, top-down and bottom-up, have complementary strengths. The combination of the two approaches has the potential to increase the sensitivity and accuracy in PTM identification and characterization. In addition, protein and PTM knowledge bases, such as UniProt, provide valuable information for PTM characterization and verification. Here, we present a software pipeline PTM-TBA (PTM characterization by Top-down and Bottom-up MS and Annotations) for identifying and localizing PTMs in proteoforms by integrating top-down and bottom-up MS as well as PTM annotations. We assessed PTM-TBA using a technical triplicate of bottom-up and top-down MS data of SW480 cells. On average, database search of the top-down MS data identified 2000 mass shifts, 814.5 (40.7%) of which were matched to 11 common PTMs and 423 of which were localized. Of the mass shifts identified by top-down MS, PTM-TBA verified 435 mass shifts using the bottom-up MS data and UniProt annotations.
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Affiliation(s)
- Wenrong Chen
- Department
of BioHealth Informatics, Indiana University-Purdue
University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Zhengming Ding
- Department
of Computer Science, Tulane School of Science and Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Yong Zang
- Department
of Biostatics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Center
for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Xiaowen Liu
- Tulane
Center for Biomedical Informatics and Genomics, Tulane University, New Orleans, Louisiana 70112, United States
- Deming Department
of Medicine, Tulane University, New Orleans, Louisiana 70112, United States
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9
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Chen W, Ding Z, Zang Y, Liu X. Characterization of proteoform post-translational modifications by top-down and bottom-up mass spectrometry in conjunction with UniProt annotations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535618. [PMID: 37066296 PMCID: PMC10104052 DOI: 10.1101/2023.04.04.535618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Many proteoforms can be produced from a gene due to genetic mutations, alternative splicing, post-translational modifications (PTMs), and other variations. PTMs in proteoforms play critical roles in cell signaling, protein degradation, and other biological processes. Mass spectrometry (MS) is the primary technique for investigating PTMs in proteoforms, and two alternative MS approaches, top-down and bottom-up, have complementary strengths. The combination of the two approaches has the potential to increase the sensitivity and accuracy in PTM identification and characterization. In addition, protein and PTM knowledgebases, such as UniProt, provide valuable information for PTM characterization and validation. Here, we present a software pipeline called PTM-TBA (PTM characterization by Top-down, Bottom-up MS and Annotations) for identifying and localizing PTMs in proteoforms by integrating top-down and bottom-up MS as well as UniProt annotations. We identified 1,662 mass shifts from a top-down MS data set of SW480 cells, 545 (33%) of which were matched to 12 common PTMs, and 351 of which were localized. PTM-TBA validated 346 of the 1,662 mass shifts using UniProt annotations or a bottom-up MS data set of SW480 cells.
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10
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Chen D, McCool EN, Yang Z, Shen X, Lubeckyj RA, Xu T, Wang Q, Sun L. Recent advances (2019-2021) of capillary electrophoresis-mass spectrometry for multilevel proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:617-642. [PMID: 34128246 PMCID: PMC8671558 DOI: 10.1002/mas.21714] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 05/06/2023]
Abstract
Multilevel proteomics aims to delineate proteins at the peptide (bottom-up proteomics), proteoform (top-down proteomics), and protein complex (native proteomics) levels. Capillary electrophoresis-mass spectrometry (CE-MS) can achieve highly efficient separation and highly sensitive detection of complex mixtures of peptides, proteoforms, and even protein complexes because of its substantial technical progress. CE-MS has become a valuable alternative to the routinely used liquid chromatography-mass spectrometry for multilevel proteomics. This review summarizes the most recent (2019-2021) advances of CE-MS for multilevel proteomics regarding technological progress and biological applications. We also provide brief perspectives on CE-MS for multilevel proteomics at the end, highlighting some future directions and potential challenges.
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Affiliation(s)
| | | | | | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Rachele A. Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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11
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Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform. Mol Cell Proteomics 2023; 22:100491. [PMID: 36603806 PMCID: PMC9944986 DOI: 10.1016/j.mcpro.2022.100491] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
Conventional proteomic approaches measure the averaged signal from mixed cell populations or bulk tissues, leading to the dilution of signals arising from subpopulations of cells that might serve as important biomarkers. Recent developments in bottom-up proteomics have enabled spatial mapping of cellular heterogeneity in tissue microenvironments. However, bottom-up proteomics cannot unambiguously define and quantify proteoforms, which are intact (i.e., functional) forms of proteins capturing genetic variations, alternatively spliced transcripts and posttranslational modifications. Herein, we described a spatially resolved top-down proteomics (TDP) platform for proteoform identification and quantitation directly from tissue sections. The spatial TDP platform consisted of a nanodroplet processing in one pot for trace samples-based sample preparation system and an laser capture microdissection-based cell isolation system. We improved the nanodroplet processing in one pot for trace samples sample preparation by adding benzonase in the extraction buffer to enhance the coverage of nucleus proteins. Using ∼200 cultured cells as test samples, this approach increased total proteoform identifications from 493 to 700; with newly identified proteoforms primarily corresponding to nuclear proteins. To demonstrate the spatial TDP platform in tissue samples, we analyzed laser capture microdissection-isolated tissue voxels from rat brain cortex and hypothalamus regions. We quantified 509 proteoforms within the union of top-down mass spectrometry-based proteoform identification and characterization and TDPortal identifications to match with features from protein mass extractor. Several proteoforms corresponding to the same gene exhibited mixed abundance profiles between two tissue regions, suggesting potential posttranslational modification-specific spatial distributions. The spatial TDP workflow has prospects for biomarker discovery at proteoform level from small tissue sections.
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12
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Cassidy L, Kaulich PT, Tholey A. Proteoforms expand the world of microproteins and short open reading frame-encoded peptides. iScience 2023; 26:106069. [PMID: 36818287 PMCID: PMC9929600 DOI: 10.1016/j.isci.2023.106069] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Microproteins and short open reading frame-encoded peptides (SEPs) can, like all proteins, carry numerous posttranslational modifications. Together with posttranscriptional processes, this leads to a high number of possible distinct protein molecules, the proteoforms, out of a limited number of genes. The identification, quantification, and molecular characterization of proteoforms possess special challenges to established, mainly bottom-up proteomics (BUP) based analytical approaches. While BUP methods are powerful, proteins have to be inferred rather than directly identified, which hampers the detection of proteoforms. An alternative approach is top-down proteomics (TDP) which allows to identify intact proteoforms. This perspective article provides a brief overview of modified microproteins and SEPs, introduces the proteoform terminology, and compares present BUP and TDP workflows highlighting their major advantages and caveats. Necessary future developments in TDP to fully accentuate its potential for proteoform-centric analytics of microproteins and SEPs will be discussed.
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Affiliation(s)
- Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Philipp T. Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany,Corresponding author
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13
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Zhang Y, Cai Q, Luo Y, Zhang Y, Li H. Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity. J Pharm Anal 2023; 13:63-72. [PMID: 36820077 PMCID: PMC9937802 DOI: 10.1016/j.jpha.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Ribosomes are abundant, large RNA-protein complexes that are the sites of all protein synthesis in cells. Defects in ribosomal proteins (RPs), including proteoforms arising from genetic variations, alternative splicing of RNA transcripts, post-translational modifications and alterations of protein expression level, have been linked to a diverse range of diseases, including cancer and aging. Comprehensive characterization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets. In the present work, using E. coli 70S RPs as an example, we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry (MS) system, and then applied it to the HeLa 80S ribosome. The results were complemented by a bottom-up approach. In total, 50 out of 55 RPs were identified using the top-down approach. Among these, more than 30 RPs were found to have their N-terminal methionine removed. Additional modifications such as methylation, acetylation, and hydroxylation were also observed, and the modification sites were identified by bottom-up MS. In a HeLa 80S ribosomal sample, we identified 98 ribosomal proteoforms, among which multiple truncated 80S ribosomal proteoforms were observed, the type of information which is often overlooked by bottom-up experiments. Although their relevance to diseases is not yet known, the integration of top-down and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets.
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Affiliation(s)
- Ying Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qinghua Cai
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yu Zhang
- The Shennong Laboratory, Zhengzhou, 450002, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- Corresponding author. School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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14
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Li N, Desiderio DM, Zhan X. The use of mass spectrometry in a proteome-centered multiomics study of human pituitary adenomas. MASS SPECTROMETRY REVIEWS 2022; 41:964-1013. [PMID: 34109661 DOI: 10.1002/mas.21710] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
A pituitary adenoma (PA) is a common intracranial neoplasm, and is a complex, chronic, and whole-body disease with multicausing factors, multiprocesses, and multiconsequences. It is very difficult to clarify molecular mechanism and treat PAs from the single-factor strategy model. The rapid development of multiomics and systems biology changed the paradigms from a traditional single-factor strategy to a multiparameter systematic strategy for effective management of PAs. A series of molecular alterations at the genome, transcriptome, proteome, peptidome, metabolome, and radiome levels are involved in pituitary tumorigenesis, and mutually associate into a complex molecular network system. Also, the center of multiomics is moving from structural genomics to phenomics, including proteomics and metabolomics in the medical sciences. Mass spectrometry (MS) has been extensively used in phenomics studies of human PAs to clarify molecular mechanisms, and to discover biomarkers and therapeutic targets/drugs. MS-based proteomics and proteoform studies play central roles in the multiomics strategy of PAs. This article reviews the status of multiomics, multiomics-based molecular pathway networks, molecular pathway network-based pattern biomarkers and therapeutic targets/drugs, and future perspectives for personalized, predeictive, and preventive (3P) medicine in PAs.
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Affiliation(s)
- Na Li
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
| | - Dominic M Desiderio
- The Charles B. Stout Neuroscience Mass Spectrometry Laboratory, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Cancer Hospital of Shandong First Medical University, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, Shandong, China
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15
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Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022; 10:proteomes10040035. [PMID: 36278695 PMCID: PMC9590004 DOI: 10.3390/proteomes10040035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Immunohistochemistry (IHC) is still widely used as a morphology-based assay for in situ analysis of target proteins as specific tumor antigens. However, as a very heterogeneous collection of neoplastic diseases, breast cancer (BC) requires an accurate identification and characterization of larger panels of candidate biomarkers, beyond ER, PR, and HER2 proteins, for diagnosis and personalized treatment, without the limited availability of antibodies that are required to identify specific proteins. Top-down, middle-down, and bottom-up mass spectrometry (MS)-based proteomics approaches complement traditional histopathological tissue analysis to examine expression, modification, and interaction of hundreds to thousands of proteins simultaneously. In this review, we discuss the proteomics-based identification of dysregulated proteins in BC that are essential for the following issues: discovery and validation of new biomarkers by analysis of solid and liquid/non-invasive biopsies, cell lines, organoids and xenograft models; identification of panels of biomarkers for early detection and accurate discrimination between cancer, benign and normal tissues; identification of subtype-specific and stage-specific protein expression profiles in BC grading and measurement of disease progression; characterization of new subtypes of BC; characterization and quantitation of post-translational modifications (PTMs) and aberrant protein-protein interactions (PPI) involved in tumor development; characterization of the global remodeling of BC tissue homeostasis, diagnosis and prognostic information; and deciphering of molecular functions, biological processes and mechanisms through which the dysregulated proteins cause tumor initiation, invasion, and treatment resistance.
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16
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Shahinuzzaman ADA, Kamal AHM, Chakrabarty JK, Rahman A, Chowdhury SM. Identification of Inflammatory Proteomics Networks of Toll-like Receptor 4 through Immunoprecipitation-Based Chemical Cross-Linking Proteomics. Proteomes 2022; 10:proteomes10030031. [PMID: 36136309 PMCID: PMC9506174 DOI: 10.3390/proteomes10030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/14/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is a receptor on an immune cell that can recognize the invasion of bacteria through their attachment with bacterial lipopolysaccharides (LPS). Hence, LPS is a pro-immune response stimulus. On the other hand, statins are lipid-lowering drugs and can also lower immune cell responses. We used human embryonic kidney (HEK 293) cells engineered to express HA-tagged TLR-4 upon treatment with LPS, statin, and both statin and LPS to understand the effect of pro- and anti-inflammatory responses. We performed a monoclonal antibody (mAb) directed co-immunoprecipitation (CO-IP) of HA-tagged TLR4 and its interacting proteins in the HEK 293 extracted proteins. We utilized an ETD cleavable chemical cross-linker to capture weak and transient interactions with TLR4 protein. We tryptic digested immunoprecipitated and cross-linked proteins on beads, followed by liquid chromatography–mass spectrometry (LC-MS/MS) analysis of the peptides. Thus, we utilized the label-free quantitation technique to measure the relative expression of proteins between treated and untreated samples. We identified 712 proteins across treated and untreated samples and performed protein network analysis using Ingenuity Pathway Analysis (IPA) software to reveal their protein networks. After filtering and evaluating protein expression, we identified macrophage myristoylated alanine-rich C kinase substrate (MARCKSL1) and creatine kinase proteins as a potential part of the inflammatory networks of TLR4. The results assumed that MARCKSL1 and creatine kinase proteins might be associated with a statin-induced anti-inflammatory response due to possible interaction with the TLR4.
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Affiliation(s)
- A. D. A. Shahinuzzaman
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Pharmaceutical Sciences Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka 1205, Bangladesh
| | - Abu Hena Mostafa Kamal
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Advanced Technology Cores, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jayanta K. Chakrabarty
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Aurchie Rahman
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Saiful M. Chowdhury
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
- Correspondence: ; Tel.: +1-817-272-5439
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17
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Plubell DL, Käll L, Webb-Robertson BJM, Bramer LM, Ives A, Kelleher NL, Smith LM, Montine TJ, Wu CC, MacCoss MJ. Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? J Proteome Res 2022; 21:891-898. [PMID: 35220718 PMCID: PMC8976764 DOI: 10.1021/acs.jproteome.1c00894] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. Commonly, a single quantitative value is reported for each protein-coding gene by aggregating peptide quantities into protein groups following protein inference or parsimony. However, given the complexity of both RNA splicing and post-translational protein modification, it is overly simplistic to assume that all peptides that map to a singular protein-coding gene will demonstrate the same quantitative response. By assuming that all peptides from a protein-coding sequence are representative of the same protein, we may miss the discovery of important biological differences. To capture the contributions of existing proteoforms, we need to reconsider the practice of aggregating protein values to a single quantity per protein-coding gene.
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Affiliation(s)
- Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Lukas Käll
- Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden
| | | | - Lisa M. Bramer
- Pacific Northwest National Laboratory, Richland, WA 99352
| | - Ashley Ives
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Neil L. Kelleher
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL 60208
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | | | - Christine C. Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
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18
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LeDuc RD, Deutsch EW, Binz PA, Fellers RT, Cesnik AJ, Klein JA, Van Den Bossche T, Gabriels R, Yalavarthi A, Perez-Riverol Y, Carver J, Bittremieux W, Kawano S, Pullman B, Bandeira N, Kelleher NL, Thomas PM, Vizcaíno JA. Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. J Proteome Res 2022; 21:1189-1195. [PMID: 35290070 PMCID: PMC7612572 DOI: 10.1021/acs.jproteome.1c00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence, including natural, chemically-induced and artifactual modifications. The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) in collaboration with several members of the Consortium for Top-Down Proteomics (CTDP) has developed a standard notation called ProForma 2.0, which is a substantial extension of the original ProForma notation developed by the CTDP. ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. ProForma 2.0 supports use cases needed for bottom-up and middle-/top-down proteomics approaches and allows the encoding of highly modified proteins and peptides using a human-and machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated by mass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical), and atomic isotopes. Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification document and information about software implementations are available at http://psidev.info/proforma.
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Affiliation(s)
- Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Pierre-Alain Binz
- Clinical Chemistry Service, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Anthony J Cesnik
- Department of Genetics, Stanford University, Stanford, California 94305, United States.,Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, California 94158, United States.,SciLifeLab, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH-Royal Institute of Technology, SE-171 21 Solna, Stockholm, Sweden 113 51
| | - Joshua A Klein
- Program for Bioinformatics, Boston University, Boston, Massachusetts 02215, United States
| | - Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark 75-FSVM II, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark 75-FSVM II, 9052 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Arshika Yalavarthi
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | | | - Shin Kawano
- Toyama University of International Studies, Toyama, 930-1292 Toyama, Higashikuromaki, 6 5-1, Japan.,Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, Chiba 277-0871, Japan
| | | | | | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60611, United States
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom
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19
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Lima DB, Dupré M, Duchateau M, Gianetto QG, Rey M, Matondo M, Chamot-Rooke J. ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment. Bioinformatics 2021; 37:2206-2208. [PMID: 33165572 DOI: 10.1093/bioinformatics/btaa958] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION We present a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. Enable rapid and easy visualization, manual validation and comparison of the identified proteoform sequences including the post-translational modification characterization. RESULTS We demonstrate the effectiveness of our approach on a large-scale Escherichia coli dataset; ProteoCombiner unambiguously shortlisted proteoforms among those identified by the multiple search engines. AVAILABILITY AND IMPLEMENTATION ProteoCombiner, a demonstration video and user tutorial are freely available at https://proteocombiner.pasteur.fr, for academic use; all data are thus available from the ProteomeXchange consortium (identifier PXD017618). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Diogo B Lima
- Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
| | - Mathieu Dupré
- Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
| | - Quentin Giai Gianetto
- Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France.,Bioinformatics and Biostatistics HUB, Computational Biology Department, Institut Pasteur, CNRS USR 3756, Paris, France
| | - Martial Rey
- Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
| | - Mariette Matondo
- Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Institut Pasteur, CNRS USR 2000, Paris, France
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20
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Abstract
Proteoform identification is required to fully understand the biological diversity present in a sample. However, these identifications are often ambiguous because of the challenges in analyzing full length proteins by mass spectrometry. A five-level proteoform classification system was recently developed to delineate the ambiguity of proteoform identifications and to allow for comparisons across software platforms and acquisition methods. Widespread adoption of this system requires software tools to provide classification of the proteoform identifications. We describe here an implementation of the five-level classification system in the software program MetaMorpheus, which provides both bottom-up and top-down identifications. Additionally, we developed a stand-alone program called ProteoformClassifier that allows users to classify proteoform results from any search program, provided that the program writes output that includes the information necessary to evaluate proteoform ambiguity. This stand-alone program includes a small test file and database to evaluate if a given program provides sufficient information to evaluate ambiguity. If the program does not, then ProteoformClassifier provides meaningful feedback to assist developers with implementing the classification system. We tested currently available top-down software programs and found that none of them (other than MetaMorpheus) provided sufficient information regarding identification ambiguity to permit classification.
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Affiliation(s)
- Zach Rolfs
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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21
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Luise A, De Cecco E, Ponzini E, Sollazzo M, Mauri P, Sobott F, Legname G, Grandori R, Santambrogio C. Profiling Dopamine-Induced Oxidized Proteoforms of β-synuclein by Top-Down Mass Spectrometry. Antioxidants (Basel) 2021; 10:antiox10060893. [PMID: 34206096 PMCID: PMC8226665 DOI: 10.3390/antiox10060893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 01/16/2023] Open
Abstract
The formation of multiple proteoforms by post-translational modifications (PTMs) enables a single protein to acquire distinct functional roles in its biological context. Oxidation of methionine residues (Met) is a common PTM, involved in physiological (e.g., signaling) and pathological (e.g., oxidative stress) states. This PTM typically maps at multiple protein sites, generating a heterogeneous population of proteoforms with specific biophysical and biochemical properties. The identification and quantitation of the variety of oxidized proteoforms originated under a given condition is required to assess the exact molecular nature of the species responsible for the process under investigation. In this work, the binding and oxidation of human β-synuclein (BS) by dopamine (DA) has been explored. Native mass spectrometry (MS) has been employed to analyze the interaction of BS with DA. In a second step, top-down fragmentation of the intact protein from denaturing conditions has been performed to identify and quantify the distinct proteoforms generated by DA-induced oxidation. The analysis of isobaric proteoforms is approached by a combination of electron-transfer dissociation (ETD) at each extent of modification, quantitation of methionine-containing fragments and combinatorial analysis of the fragmentation products by multiple linear regression. This procedure represents a promising approach to systematic assessment of proteoforms variety and their relative abundance. The method can be adapted, in principle, to any protein containing any number of methionine residues, allowing for a full structural characterization of the protein oxidation states.
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Affiliation(s)
- Arianna Luise
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Elena De Cecco
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
- ELETTRA-Sincrotrone Trieste S.C.p.A, Basovizza, 34149 Trieste, Italy
| | - Erika Ponzini
- Department of Materials Science, University of Milano-Bicocca, 20125 Milan, Italy
| | - Martina Sollazzo
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
- ELETTRA-Sincrotrone Trieste S.C.p.A, Basovizza, 34149 Trieste, Italy
| | - PierLuigi Mauri
- Institute of Biomedical Technologies, National Research Council of Italy, Segrate, 20090 Milan, Italy
| | - Frank Sobott
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
- ELETTRA-Sincrotrone Trieste S.C.p.A, Basovizza, 34149 Trieste, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
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22
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Quantitative proteomics characterization of cancer biomarkers and treatment. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:255-263. [PMID: 34095463 PMCID: PMC8142045 DOI: 10.1016/j.omto.2021.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cancer accounted for 16% of all death worldwide in 2018. Significant progress has been made in understanding tumor occurrence, progression, diagnosis, treatment, and prognosis at the molecular level. However, genomics changes cannot truly reflect the state of protein activity in the body due to the poor correlation between genes and proteins. Quantitative proteomics, capable of quantifying the relatively different protein abundance in cancer patients, has been increasingly adopted in cancer research. Quantitative proteomics has great application potentials, including cancer diagnosis, personalized therapeutic drug selection, real-time therapeutic effects and toxicity evaluation, prognosis and drug resistance evaluation, and new therapeutic target discovery. In this review, the development, testing samples, and detection methods of quantitative proteomics are introduced. The biomarkers identified by quantitative proteomics for clinical diagnosis, prognosis, and drug resistance are reviewed. The challenges and prospects of quantitative proteomics for personalized medicine are also discussed.
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23
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Thomas SL, Thacker JB, Schug KA, Maráková K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci 2020; 44:211-246. [DOI: 10.1002/jssc.202000936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shannon L. Thomas
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Jonathan B. Thacker
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Kevin A. Schug
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy Faculty of Pharmacy Comenius University in Bratislava Bratislava Slovakia
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