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Nitika, Porter CM, Truman AW, Truttmann MC. Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code. J Biol Chem 2020; 295:10689-10708. [PMID: 32518165 PMCID: PMC7397107 DOI: 10.1074/jbc.rev120.011666] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/08/2020] [Indexed: 02/01/2023] Open
Abstract
Cells must be able to cope with the challenge of folding newly synthesized proteins and refolding those that have become misfolded in the context of a crowded cytosol. One such coping mechanism that has appeared during evolution is the expression of well-conserved molecular chaperones, such as those that are part of the heat shock protein 70 (Hsp70) family of proteins that bind and fold a large proportion of the proteome. Although Hsp70 family chaperones have been extensively examined for the last 50 years, most studies have focused on regulation of Hsp70 activities by altered transcription, co-chaperone "helper" proteins, and ATP binding and hydrolysis. The rise of modern proteomics has uncovered a vast array of post-translational modifications (PTMs) on Hsp70 family proteins that include phosphorylation, acetylation, ubiquitination, AMPylation, and ADP-ribosylation. Similarly to the pattern of histone modifications, the histone code, this complex pattern of chaperone PTMs is now known as the "chaperone code." In this review, we discuss the history of the Hsp70 chaperone code, its currently understood regulation and functions, and thoughts on what the future of research into the chaperone code may entail.
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Affiliation(s)
- Nitika
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina, USA
| | - Corey M Porter
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina, USA
| | - Matthias C Truttmann
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Geriatrics Center, University of Michigan, Ann Arbor, Michigan, USA
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52
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Itze-Mayrhofer C, Brem G. Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids. J Proteomics 2020; 225:103884. [PMID: 32593762 DOI: 10.1016/j.jprot.2020.103884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 02/06/2023]
Abstract
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
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Affiliation(s)
- Corina Itze-Mayrhofer
- Institute of Animal Breeding and Genetics, Group Molecular Reproduction IFA-Tulln, University of Veterinary Medicine, Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
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53
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Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)-Based Proteomics of Drug-Metabolizing Enzymes and Transporters. Molecules 2020; 25:molecules25112718. [PMID: 32545386 PMCID: PMC7321193 DOI: 10.3390/molecules25112718] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples, outperforming conventional antibody-based methods in many aspects. LC-MS/MS-based proteomics studies have revealed the protein abundances of many drug-metabolizing enzymes and transporters (DMETs) in tissues relevant to drug metabolism and disposition. Previous studies have consistently demonstrated marked interindividual variability in DMET protein expression, suggesting that varied DMET function is an important contributing factor for interindividual variability in pharmacokinetics (PK) and pharmacodynamics (PD) of medications. Moreover, differential DMET expression profiles were observed across different species and in vitro models. Therefore, caution must be exercised when extrapolating animal and in vitro DMET proteomics findings to humans. In recent years, DMET proteomics has been increasingly utilized for the development of physiologically based pharmacokinetic models, and DMET proteins have also been proposed as biomarkers for prediction of the PK and PD of the corresponding substrate drugs. In sum, despite the existence of many challenges in the analytical technology and data analysis methods of LC-MS/MS-based proteomics, DMET proteomics holds great potential to advance our understanding of PK behavior at the individual level and to optimize treatment regimens via the DMET protein biomarker-guided precision pharmacotherapy.
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54
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Hu J, Zheng Q. Applications of Mass Spectrometry in the Onset of Amyloid Fibril Formation: Focus on the Analysis of Early-Stage Oligomers. Front Chem 2020; 8:324. [PMID: 32432078 PMCID: PMC7215083 DOI: 10.3389/fchem.2020.00324] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/30/2020] [Indexed: 02/05/2023] Open
Abstract
Amyloid fibril formation is a hallmark of diverse neurodegenerative and metabolic diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), and type 2 diabetes mellitus (T2DM). Conventional diagnosis is based on the appearance of fibrils or plaques, while neglects the role of early-stage oligomers in the disease progression. Recent studies have uncovered that it is the early-stage oligomer, rather than the mature fibril, that greatly contributes cytotoxicity. The formation of oligomers involves complicate structural conversions and it is essential to investigate their conformational changes for a better understanding of aggregation mechanism. The coexistence of soluble early-stage oligomers, intermediates, and pre-fibril species makes it difficult to be differentiate by morphological methods, and only average structural information is provided as they lack the ability of separation. Therefore, mass spectrometry (MS) becomes an alternative technique that presents new and complementary insights into the onset of amyloid fibrils. This review highlights the hotspots and important achievements by MS in the field of amyloid formation mechanism, including the direct detection and differentiation of soluble oligomers (native MS), unambiguous identification of interacted sites involved in the onset of aggregation [hydrogen/deuterium exchange (HDX) and chemical cross-linking (CX)], and conformational switch that leads to fibrilization [collision cross section (CCS) regularity by ion mobility (IM)].
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Affiliation(s)
- Jiaojiao Hu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qiuling Zheng
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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55
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Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int J Mol Sci 2020; 21:ijms21041524. [PMID: 32102244 PMCID: PMC7073195 DOI: 10.3390/ijms21041524] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.
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56
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Jin Y, Diffee GM, Colman RJ, Anderson RM, Ge Y. Top-down Mass Spectrometry of Sarcomeric Protein Post-translational Modifications from Non-human Primate Skeletal Muscle. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2460-2469. [PMID: 30834509 PMCID: PMC6722035 DOI: 10.1007/s13361-019-02139-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 05/22/2023]
Abstract
Sarcomeric proteins, including myofilament and Z-disk proteins, play critical roles in regulating muscle contractile properties. A variety of isoforms and post-translational modifications (PTMs) of sarcomeric proteins have been shown to be associated with modulation of muscle functions and the occurrence of muscle diseases. Non-human primates (NHPs) are excellent research models for sarcopenia, a disease associated with alterations in sarcomeric proteins, due to their marked similarities to humans. However, the sarcomeric proteins in NHP skeletal muscle have not been well characterized. To gain a deeper understanding of sarcomeric proteins in NHP skeletal muscle, we employed top-down mass spectrometry (MS) to conduct a comprehensive analysis on isoforms and PTMs of sarcomeric proteins in rhesus macaque skeletal muscle. We identified 23 protein isoforms with 46 proteoforms of sarcomeric proteins, including 6 isoforms with 18 proteoforms from fast skeletal troponin T. Particularly, for the first time, a novel PDZ/LIM domain protein isoform, PDLIM7, was characterized with a newly identified protein sequence. Moreover, we also identified multiple PTMs on these proteins, including deamidation, methylation, acetylation, tri-methylation, phosphorylation, and S-glutathionylation. Most PTM sites were localized, including Asn13 deamidation on MLC-2S; His73 methylation on αactin; N-terminal acetylation on most identified proteins; N-terminal tri-methylation on MLC-1S, MLC-1F, MLC-2S, and MLC-2F; Ser14 phosphorylation on MLC-2S; and Ser15 and Ser16 phosphorylation on MLC-2F. In summary, a comprehensive characterization of sarcomeric proteins including multiple isoforms and PTMs in NHP skeletal muscle was achieved by analyzing intact proteins in the top-down MS approach.
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Affiliation(s)
- Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gary M Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ricki J Colman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Rozalyn M Anderson
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, 53705, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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57
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Sanders JD, Mullen C, Watts E, Holden DD, Syka JEP, Schwartz JC, Brodbelt JS. Enhanced Sequence Coverage of Large Proteins by Combining Ultraviolet Photodissociation with Proton Transfer Reactions. Anal Chem 2019; 92:1041-1049. [DOI: 10.1021/acs.analchem.9b04026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- James D. Sanders
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Eleanor Watts
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dustin D. Holden
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - John E. P. Syka
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jae C. Schwartz
- Thermo Fisher Scientific Inc., 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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58
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Melby JA, Jin Y, Lin Z, Tucholski T, Wu Z, Gregorich ZR, Diffee GM, Ge Y. Top-Down Proteomics Reveals Myofilament Proteoform Heterogeneity among Various Rat Skeletal Muscle Tissues. J Proteome Res 2019; 19:446-454. [PMID: 31647247 DOI: 10.1021/acs.jproteome.9b00623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heterogeneity in skeletal muscle contraction time, peak power output, and resistance to fatigue, among others, is necessary to accommodate the wide range of functional demands imposed on the body. Underlying this functional heterogeneity are a myriad of differences in the myofilament protein isoform expression and post-translational modifications; yet, characterizing this heterogeneity remains challenging. Herein, we have utilized top-down liquid chromatography (LC)-mass spectrometry (MS)-based proteomics to characterize myofilament proteoform heterogeneity in seven rat skeletal muscle tissues including vastus lateralis, vastus medialis, vastus intermedius, rectus femoris, soleus, gastrocnemius, and plantaris. Top-down proteomics revealed that myofilament proteoforms varied greatly across the seven different rat skeletal muscle tissues. Subsequently, we quantified and characterized myofilament proteoforms using online LC-MS. We have comprehensively characterized the fast and slow skeletal troponin I isoforms, which demonstrates the ability of top-down MS to decipher isoforms with high sequence homology. Taken together, we have shown that top-down proteomics can be used as a robust and high-throughput method to characterize the molecular heterogeneity of myofilament proteoforms from various skeletal muscle tissues.
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59
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Zeng Y, Wang S, Feng M, Shao Z, Yuan J, Shen Z, Jie W. [Quantitative proteomics and differential signal enrichment in nasopharyngeal carcinoma cells with or without SETD2 gene knockout]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:1191-1199. [PMID: 31801714 DOI: 10.12122/j.issn.1673-4254.2019.10.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To analyze the effects of alterations in the expressions of methyltransferase SETD2 on protein expression profiles in human nasopharyngeal carcinoma (NPC) cells and enrich the differential signaling pathways. METHODS The total protein was extracted from SETD2-knockout cell line CNE1SETD2-KO and the wild-type cell line CNE1WT, and the differentially expressed proteins were screened by tandem mass tag (TMT) labeled protein quantification technique and tandem mass spectrometry. GO analysis was used to annotate and enrich the differentially expressed proteins, and the KEGG database was used to enrich and analyze the pathways of the differential proteins. RESULTS With a fold change (FC)≥1.2 and P < 0.05 as the screening standard, 2049 differentially expressed proteins were identified in CNE1SETD2-KO cells, among which 904 were up-regulated and 1145 were down-regulated. GO functional annotation results indicated that SETD2 knockout caused characteristic changes in multiple biological processes (cell processes and regulation, cell movement, metabolic processes, and biosynthesis of cellular components), molecular functions (catalytic activity and molecular binding, transcription factor activity), and cellular components (cell membrane, organelle, macromolecular complex). KEGG analysis showed that the differentially expressed proteins were involved in an array of signaling pathways closely related to tumors, including MAPK, PI3K-Akt, Ras, Rap1, mTOR, Hippo, HIF-1, Wnt, AMPK, FoxO, ErbB, P53 and JAK-STAT. CONCLUSIONS SETD2 knockout significantly changes the protein expression characteristics of NPC cells and affects a number of signal pathways closely related to tumors. The results provide evidence for investigation of the pathogenesis and therapeutic target screening of NPC.
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Affiliation(s)
- Yumei Zeng
- Department of Pathology, Zhongshan People's Hospital, Zhongshan 528400, China
| | - Sisi Wang
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang 524023, China
| | - Muyin Feng
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang 524023, China
| | - Zhongming Shao
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang 524023, China
| | - Jianling Yuan
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang 524023, China
| | - Zhihua Shen
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang 524023, China
| | - Wei Jie
- Department of Pathology, School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang 524023, China
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60
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A new paradigm in public health assessment: Water fingerprinting for protein markers of public health using mass spectrometry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115621] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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61
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Wang C, Zou P, Yang C, Liu L, Cheng L, He X, Zhang L, Zhang Y, Jiang H, Chen PR. Dynamic modifications of biomacromolecules: mechanism and chemical interventions. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1459-1471. [PMID: 31555961 DOI: 10.1007/s11427-019-9823-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 08/20/2019] [Indexed: 01/24/2023]
Abstract
Biological macromolecules (proteins, nucleic acids, polysaccharides, etc.) are the building blocks of life, which constantly undergo chemical modifications that are often reversible and spatial-temporally regulated. These dynamic properties of chemical modifications play fundamental roles in physiological processes as well as pathological changes of living systems. The Major Research Project (MRP) funded by the National Natural Science Foundation of China (NSFC)-"Dynamic modifications of biomacromolecules: mechanism and chemical interventions" aims to integrate cross-disciplinary approaches at the interface of chemistry, life sciences, medicine, mathematics, material science and information science with the following goals: (i) developing specific labeling techniques and detection methods for dynamic chemical modifications of biomacromolecules, (ii) analyzing the molecular mechanisms and functional relationships of dynamic chemical modifications of biomacromolecules, and (iii) exploring biomacromolecules and small molecule probes as potential drug targets and lead compounds.
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Affiliation(s)
- Chu Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Caiguang Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lei Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Liang Cheng
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiaopeng He
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Zhang
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Hualiang Jiang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Peng R Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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Álvarez JV, Bravo SB, García-Vence M, De Castro MJ, Luzardo A, Colón C, Tomatsu S, Otero-Espinar FJ, Couce ML. Proteomic Analysis in Morquio A Cells Treated with Immobilized Enzymatic Replacement Therapy on Nanostructured Lipid Systems. Int J Mol Sci 2019; 20:ijms20184610. [PMID: 31540344 PMCID: PMC6769449 DOI: 10.3390/ijms20184610] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/07/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022] Open
Abstract
Morquio A syndrome, or mucopolysaccharidosis type IVA (MPS IVA), is a lysosomal storage disease due to mutations in the N-acetylgalactosamine-6-sulfatase (GALNS) gene. Systemic skeletal dysplasia and the related clinical features of MPS IVA are due to disruption of cartilage and its extracellular matrix, leading to an imbalance of growth. Enzyme replacement therapy (ERT) with recombinant human GALNS, alpha elosulfase, provides a systemic treatment. However, this therapy has a limited impact on skeletal dysplasia because the infused enzyme cannot penetrate cartilage and bone. Therefore, an alternative therapeutic approach to reach the cartilage is an unmet challenge. We have developed a new drug delivery system based on a nanostructure lipid carrier with the capacity to immobilize enzymes used for ERT and to target the lysosomes. This study aimed to assess the effect of the encapsulated enzyme in this new delivery system, using in vitro proteomic technology. We found a greater internalization of the enzyme carried by nanoparticles inside the cells and an improvement of cellular protein routes previously impaired by the disease, compared with conventional ERT. This is the first qualitative and quantitative proteomic assay that demonstrates the advantages of a new delivery system to improve the MPS IVA ERT.
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Affiliation(s)
- J Víctor Álvarez
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Campus Vida, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain.
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
- Skeletal Dysplasia Lab Nemours Biomedical Research Nemours/Alfred I. duPont Hospital for Children, 1600 Rockland Road, Wilmington, DE 19803, USA.
| | - Susana B Bravo
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostea, Spain.
| | - María García-Vence
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostea, Spain.
| | - María J De Castro
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
| | - Asteria Luzardo
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Sciences, Campus de Lugo, University of Santiago de Compostela, 27002 Lugo, Spain.
- Paraquasil Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain.
| | - Cristóbal Colón
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
| | - Shunji Tomatsu
- Skeletal Dysplasia Lab Nemours Biomedical Research Nemours/Alfred I. duPont Hospital for Children, 1600 Rockland Road, Wilmington, DE 19803, USA.
| | - Francisco J Otero-Espinar
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, School of Pharmacy, Campus Vida, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain.
- Paraquasil Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain.
| | - María L Couce
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Paediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain.
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63
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Chen B, Lin Z, Zhu Y, Jin Y, Larson E, Xu Q, Fu C, Zhang Z, Zhang Q, Pritts WA, Ge Y. Middle-Down Multi-Attribute Analysis of Antibody-Drug Conjugates with Electron Transfer Dissociation. Anal Chem 2019; 91:11661-11669. [PMID: 31442030 DOI: 10.1021/acs.analchem.9b02194] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antibody-drug conjugates (ADCs) are designed to combine the target specificity of monoclonal antibodies and potent cytotoxin drugs to achieve better therapeutic outcomes. Comprehensive evaluation of the quality attributes of ADCs is critical for drug development but remains challenging due to heterogeneity of the construct. Currently, peptide mapping with reversed-phase liquid chromatography (RPLC) coupled to mass spectrometry (MS) is the predominant approach to characterize ADCs. However, it is suboptimal for sequence characterization and quantification of ADCs because it lacks a comprehensive view of coexisting variants and suffers from varying ionization effects of drug-conjugated peptides compared to unconjugated counterparts. Here, we present the first middle-down RPLC-MS analysis of both cysteine (Adcetris; BV) and lysine (Kadcyla; T-DM1) conjugated ADCs at the subunit level (∼25 kDa) with electron transfer dissociation (ETD). We successfully achieved high-resolution separation of subunit isomers arising from different drug conjugation and subsequently localized the conjugation sites. Moreover, we obtained a comprehensive overview of the microvariants associated with each subunits and characterized them such as oxidized variants with different sites. Furthermore, we observed relatively high levels of conjugation near complementarity-determining regions (CDRs) from the heavy chain but no drug conjugation near CDRs of light chain (Lc) from lysine conjugated T-DM1. Based on the extracted ion chromatograms, we accurately measured average drug to antibody ratio (DAR) values and relative occupancy of drug-conjugated subunits. Overall, the middle-down MS approach enables the evaluation of multiple quality attributes including DAR, positional isomers, conjugation sites, occupancy, and microvariants, which potentially opens up a new avenue to characterize ADCs.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Yutong Jin
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Eli Larson
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Qingge Xu
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Cexiong Fu
- Process Analytical , AbbVie Inc. , North Chicago , Illinois 60064 , United States
| | - Zhaorui Zhang
- Process Analytical , AbbVie Inc. , North Chicago , Illinois 60064 , United States
| | - Qunying Zhang
- Process Analytical , AbbVie Inc. , North Chicago , Illinois 60064 , United States
| | - Wayne A Pritts
- Process Analytical , AbbVie Inc. , North Chicago , Illinois 60064 , United States
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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Yao B, Liu J, Xu D, Pan D, Zhang M, Zhao D, Leng X. Dissection of the molecular targets and signaling pathways of Guzhi Zengsheng Zhitongwan based on the analysis of serum proteomics. Chin Med 2019; 14:29. [PMID: 31485261 PMCID: PMC6712859 DOI: 10.1186/s13020-019-0252-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
Background Guzhi Zengsheng Zhitongwan (GZZSZTW) is an effective formula of traditional Chinese herbal medicine and has been widely applied in the treatment of joint diseases for many years. The aim of this study was to dissect the molecular targets and signaling pathways of Guzhi Zengsheng Zhitongwan based on the analysis of serum proteomics. Methods The Chinese herbs of GZZSZTW were immersed in 5 l distilled water and boiled with reflux extraction method. The extract was filtered, concentrated and freeze-dried. The chemical profile of GZZSZTW extract was determined by high-performance lipid chromatography (HPLC). The 7-week old Sprague-Dawley (SD) rats in GZZSZTW groups were received oral administration at doses of 0.8, 1.05, and 1.3 g/kg per day and the rats in blank group were fed with drinking water. Serum samples were collected from the jugular veins. Primary chondrocyte viability was evaluated by CCK-8 assay. A full spectrum of the molecular targets and signaling pathways of GZZSZTW were investigated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis and a systematic bioinformatics analysis accompanied with parallel reaction monitoring (PRM) and siRNA validation. Results GZZSZTW regulated a series of functional proteins and signaling pathways responsible for cartilage development, growth and repair. Functional classification analysis indicated that these proteins were mainly involved in the process of cell surface dynamics. Pathway analysis mapped these proteins into several signalling pathways involved in chondrogenesis, chondrocyte proliferation and differentiation, and cartilage repair, including hippo signaling pathway, cGMP-PKG signaling pathway, cell cycle and calcium signaling pathway. Protein–protein interaction analysis and siRNA knockdown assay identified an interaction network consisting of TGFB1, RHO GTPases, ILK, FLNA, LYN, DHX15, PKM, RAB15, RAB1B and GIPC1. Conclusions Our results suggest that the effects of GZZSZTW on treating joint diseases might be achieved through the TGFB1/RHO interaction network coupled with other proteins and signaling pathways responsible for cartilage development, growth and repair. Therefore, the present study has greatly expanded our knowledge and provided scientific support for the underlying therapeutic mechanisms of GZZSZTW on treating joint diseases. It also provided possible alternative strategies for the prevention and treatment for joint diseases by using traditional Chinese herbal formulas.
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Affiliation(s)
- Baojin Yao
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Jia Liu
- 2College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Duoduo Xu
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Daian Pan
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Mei Zhang
- 3Innovation Practice Center, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Daqing Zhao
- 1Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
| | - Xiangyang Leng
- 4The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 130117 Jilin China
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65
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Top-Down Proteomics Applied to Human Cerebrospinal Fluid. Methods Mol Biol 2019. [PMID: 31432414 DOI: 10.1007/978-1-4939-9706-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cerebrospinal fluid (CSF) is the fluid of choice to study pathologies and disorders of the central nervous system (CNS). Its composition, especially its proteins and peptides, holds the promise that it may reflect the pathological state of an individual. Traditionally, proteins and peptides in CSF have been analyzed using bottom-up proteomics technologies in the search of high proteome coverage. However, the limited protein sequence coverage of this technology means that information regarding post-translational modifications (PTMs) and alternative splice variants is lost. As an alternative technology, top-down proteomics offers low to medium proteome coverage, but high protein coverage enabling almost a full characterization of the proteins' primary structure. This allows us to precisely identify distinct molecular forms of proteins (proteoforms) as well as naturally occurring bioactive peptide fragments, which could be of critical biological relevance and would otherwise remain undetected with a classical proteomics approach.Here, we describe various strategies including sample preparation protocols, off-line intact protein prefractionation, and LC-MS/MS methods together with data analysis pipelines to analyze cerebrospinal fluid (CSF) by top-down proteomics. However, there is not a unique or standardized method and the selection of the top-down strategy will depend on the exact goal of the study. Here, we describe various top-down proteomics methods that enable rapid protein characterization and may be an excellent companion analytical workflow in the search for new protein biomarkers in neurodegenerative diseases.
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66
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SPECTRUM - A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data. Sci Rep 2019; 9:11267. [PMID: 31375721 PMCID: PMC6677810 DOI: 10.1038/s41598-019-47724-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry. TDP has an edge over other proteomics protocols in that it allows for: (i) accurate measurement of intact protein mass, (ii) high sequence coverage, and (iii) enhanced identification of post-translational modifications (PTMs). However, the complexity of TDP spectra poses a significant impediment to protein search and PTM characterization. Furthermore, limited software support is currently available in the form of search algorithms and pipelines. To address this need, we propose ‘SPECTRUM’, an open-architecture and open-source toolbox for TDP data analysis. Its salient features include: (i) MS2-based intact protein mass tuning, (ii) de novo peptide sequence tag analysis, (iii) propensity-driven PTM characterization, (iv) blind PTM search, (v) spectral comparison, (vi) identification of truncated proteins, (vii) multifactorial coefficient-weighted scoring, and (viii) intuitive graphical user interfaces to access the aforementioned functionalities and visualization of results. We have validated SPECTRUM using published datasets and benchmarked it against salient TDP tools. SPECTRUM provides significantly enhanced protein identification rates (91% to 177%) over its contemporaries. SPECTRUM has been implemented in MATLAB, and is freely available along with its source code and documentation at https://github.com/BIRL/SPECTRUM/.
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67
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Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
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68
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He Y, Mohamedali A, Huang C, Baker MS, Nice EC. Oncoproteomics: Current status and future opportunities. Clin Chim Acta 2019; 495:611-624. [PMID: 31176645 DOI: 10.1016/j.cca.2019.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early clinical stage cancer detection, targeted molecular therapies, disease monitoring, and drug development. Such information will lead to new understandings of cancer biology and impact dramatically on the future care of cancer patients. In this review, we will summarize the advantages and limitations of the key technologies used in (onco)proteogenomics, (the Omics Pipeline), explain how they can assist us in understanding the biology behind the overarching "Hallmarks of Cancer", discuss how they can advance the development of precision/personalised medicine and the future directions in the field.
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Affiliation(s)
- Yujia He
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Canhua Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia.
| | - Edouard C Nice
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
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69
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Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics 2019; 19:e1800361. [PMID: 31050378 PMCID: PMC6602557 DOI: 10.1002/pmic.201800361] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/07/2019] [Indexed: 12/29/2022]
Abstract
A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post-translational modifications. In top-down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top-down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.
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Affiliation(s)
- Leah V. Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Robert J. Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rachel M. Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Ryan T. Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry and Molecular Biosciences and the Division of Hematology-Oncology, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard D. LeDuc
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Samuel H. Payne
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Paul M. Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Michael R. Shortreed
- 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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70
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Mezger STP, Mingels AMA, Bekers O, Cillero-Pastor B, Heeren RMA. Trends in mass spectrometry imaging for cardiovascular diseases. Anal Bioanal Chem 2019; 411:3709-3720. [PMID: 30980090 PMCID: PMC6594994 DOI: 10.1007/s00216-019-01780-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 01/01/2023]
Abstract
Mass spectrometry imaging (MSI) is a widely established technology; however, in the cardiovascular research field, its use is still emerging. The technique has the advantage of analyzing multiple molecules without prior knowledge while maintaining the relation with tissue morphology. Particularly, MALDI-based approaches have been applied to obtain in-depth knowledge of cardiac (dys)function. Here, we discuss the different aspects of the MSI protocols, from sample handling to instrumentation used in cardiovascular research, and critically evaluate these methods. The trend towards structural lipid analysis, identification, and “top-down” protein MSI shows the potential for implementation in (pre)clinical research and complementing the diagnostic tests. Moreover, new insights into disease progression are expected and thereby contribute to the understanding of underlying mechanisms related to cardiovascular diseases.
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Affiliation(s)
- Stephanie T P Mezger
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.,Central Diagnostic Laboratory, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Alma M A Mingels
- Central Diagnostic Laboratory, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Otto Bekers
- Central Diagnostic Laboratory, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.,CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Berta Cillero-Pastor
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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71
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Lin Z, Wei L, Cai W, Zhu Y, Tucholski T, Mitchell SD, Guo W, Ford SP, Diffee GM, Ge Y. Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome. Mol Cell Proteomics 2019; 18:594-605. [PMID: 30591534 PMCID: PMC6398208 DOI: 10.1074/mcp.tir118.001086] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Determining changes in protein expression and post-translational modifications (PTMs) is crucial for elucidating cellular signal transduction and disease mechanisms. Conventional antibody-based approaches have inherent problems such as the limited availability of high-quality antibodies and batch-to-batch variation. Top-down mass spectrometry (MS)-based proteomics has emerged as the most powerful method for characterization and quantification of protein modifications. Nevertheless, robust methods to simultaneously determine changes in protein expression and PTMs remain lacking. Herein, we have developed a straightforward and robust top-down liquid chromatography (LC)/MS-based targeted proteomics platform for simultaneous quantification of protein expression and PTMs with high throughput and high reproducibility. We employed this method to analyze the sarcomeric subproteome from various muscle types of different species, which successfully revealed skeletal muscle heterogeneity and cardiac developmental changes in sarcomeric protein isoform expression and PTMs. As demonstrated, this targeted top-down proteomics platform offers an excellent 'antibody-independent' alternative for the accurate quantification of sarcomeric protein expression and PTMs concurrently in complex mixtures, which is generally applicable to different species and various tissue types.
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Affiliation(s)
- Ziqing Lin
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Liming Wei
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ¶Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Yanlong Zhu
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Trisha Tucholski
- **Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Stanford D Mitchell
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Wei Guo
- ‡‡Department of Animal Science, Fetal Programming Center, University of Wyoming, Laramie, Wyoming 82071
| | - Stephen P Ford
- ‡‡Department of Animal Science, Fetal Programming Center, University of Wyoming, Laramie, Wyoming 82071
| | - Gary M Diffee
- §§Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53705
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705;
- §Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
- ‖Molecular & Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705
- **Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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72
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Structural mass spectrometry comes of age: new insight into protein structure, function and interactions. Biochem Soc Trans 2019; 47:317-327. [DOI: 10.1042/bst20180356] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022]
Abstract
Abstract
Mass spectrometry (MS) provides an impressive array of information about the structure, function and interactions of proteins. In recent years, many new developments have been in the field of native MS and these exemplify a new coming of age of this field. In this mini review, we connect the latest methodological and instrumental developments in native MS to the new insights these have enabled. We highlight the prominence of an increasingly common strategy of using hybrid approaches, where multiple MS-based techniques are used in combination, and integrative approaches, where MS is used alongside other techniques such as ion-mobility spectrometry. We also review how the emergence of a native top-down approach, which combines native MS with top-down proteomics into a single experiment, is the pièce de résistance of structural mass spectrometry's coming of age. Finally, we outline key developments that have enabled membrane protein native MS to shift from being extremely challenging to routine, and how this technique is uncovering inaccessible details of membrane protein–lipid interactions.
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73
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Microbial Proteomics and Their Importance in Medical Microbiology. RECENT DEVELOPMENTS IN APPLIED MICROBIOLOGY AND BIOCHEMISTRY 2019. [PMCID: PMC7149639 DOI: 10.1016/b978-0-12-816328-3.00003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial infection is a leading cause of death around the world. Most of the infectious diseases are caused by drug-resistant microbes; this may lead to a delay in the administration of microbiologically effective therapy (Chen et al., 2017; Del Chierico et al., 2014). Therefore, exhaustive understanding of microbial physiologies, infection and defense systems, and survival strategies is of great interest in order to actively defeat microbial infection. Microbial proteomics provides complete information of microbial physiology and expression and function of the proteins that are involved in infection and also gives a clue in clinical diagnosis and antimicrobial therapy (Pérez-Llarena and Bou, 2016; Vranakis et al., 2014). Microbial proteomics helps to identify the proteins associated with microbial activity, microbial host-pathogen interactions, and antimicrobial resistant mechanism. Microbial activity of pathogens can be confirmed by using the 2-D gel-based and gel-free method with the combination of MALDI-TOF-LC-MS/MS. Proteomic analysis of microbial host-pathogen interaction reveals valuable information about the virulence of the pathogen and its resistance; it helps in better understanding of the infection and for developing strategies against microbial infections (Cheng et al., 2016). Fig. 3.1 schematically illustrates the proteomic analysis of the bacterial samples.
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74
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Inventory of proteoforms as a current challenge of proteomics: Some technical aspects. J Proteomics 2019; 191:22-28. [DOI: 10.1016/j.jprot.2018.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 02/08/2023]
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75
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Orlando E, Aebersold R. On the contribution of mass spectrometry-based platforms to the field of personalized oncology. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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76
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Coelho Graça D, Hartmer R, Jabs W, Scherl A, Clerici L, Samii K, Tsybin YO, Hochstrasser D, Lescuyer P. Detection of Proteoforms Using Top-Down Mass Spectrometry and Diagnostic Ions. Methods Mol Biol 2019; 1959:173-183. [PMID: 30852823 DOI: 10.1007/978-1-4939-9164-8_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Characterization of protein structure modifications is an important field in mass spectrometry (MS)-based proteomics. Here, we describe a process to quickly and reliably identify a mass change in a targeted protein sequence by top-down mass spectrometry (TD MS) using electron transfer dissociation (ETD). The step-by-step procedure describes how to develop a TD MS method for data acquisition as well as the data analysis process. The described TD MS workflow utilizes diagnostic ions to characterize an unknown sample in a few hours.
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Affiliation(s)
- Didia Coelho Graça
- Clinical Proteomics and Chemistry Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Department of Genetic, Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland.
| | | | - Wolfgang Jabs
- Beuth Hochschule für Technik Berlin, Berlin, Germany
| | - Alexander Scherl
- Clinical Proteomics and Chemistry Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Genetic, Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Lorella Clerici
- Department of Genetic, Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Kaveh Samii
- Department of Genetic, Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
- Division of Hematology, Geneva University Hospitals, Geneva, Switzerland
| | | | - Denis Hochstrasser
- Clinical Proteomics and Chemistry Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Genetic, Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Pierre Lescuyer
- Clinical Proteomics and Chemistry Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Genetic, Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
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77
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Mass Spectrometry-Based Biomarkers in Drug Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:435-449. [PMID: 31347063 DOI: 10.1007/978-3-030-15950-4_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Advances in mass spectrometry, proteomics, protein bioanalytical approaches, and biochemistry have led to a rapid evolution and expansion in the area of mass spectrometry-based biomarker discovery and development. The last decade has also seen significant progress in establishing accepted definitions, guidelines, and criteria for the analytical validation, acceptance and qualification of biomarkers. These advances have coincided with a decreased return on investment for pharmaceutical research and development and an increasing need for better early decision making tools. Empowering development teams with tools to measure a therapeutic interventions impact on disease state and progression, measure target engagement and to confirm predicted pharmacodynamic effects is critical to efficient data-driven decision making. Appropriate implementation of a biomarker or a combination of biomarkers can enhance understanding of a drugs mechanism, facilitate effective translation from the preclinical to clinical space, enable early proof of concept and dose selection, and increases the efficiency of drug development. Here we will provide descriptions of the different classes of biomarkers that have utility in the drug development process as well as review specific, protein-centric, mass spectrometry-based approaches for the discovery of biomarkers and development of targeted assays to measure these markers in a selective and analytically precise manner.
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78
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Wang Y, Olesik SV. Enhanced-Fluidity Liquid Chromatography-Mass Spectrometry for Intact Protein Separation and Characterization. Anal Chem 2018; 91:935-942. [PMID: 30523683 DOI: 10.1021/acs.analchem.8b03970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent advances in the analysis of proteins have increased the demand for more efficient techniques to separate intact proteins. Enhanced-fluidity liquid chromatography (EFLC) involves the addition of liquefied CO2 to conventional liquid mobile phases. The addition of liquefied CO2 increases diffusivity and decreases viscosity, which inherently leads to a more efficient separation. Herein, EFLC is applied to hydrophobic interaction chromatography (HIC) stationary phases for the first time to study the impact of liquefied CO2 to the chromatographic behavior of proteins. The effects of liquefied CO2 on chromatographic properties, charge state distributions (CSDs), and ionization efficiencies were evaluated. EFLC offered improved chromatographic performance compared to conventional liquid chromatography (LC) methods including a shorter analysis time, better peak shapes, and higher plate numbers. The addition of liquefied CO2 to the mobile phase provided an electrospray ionization (ESI)-friendly and "supercharging" reagent without sacrificing chromatographic performance, which can be used to improve peptide and protein identification in large-scale application.
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Affiliation(s)
- Yanhui Wang
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States of America
| | - Susan V Olesik
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States of America
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Tans R, Verschuren L, Wessels HJCT, Bakker SJL, Tack CJ, Gloerich J, van Gool AJ. The future of protein biomarker research in type 2 diabetes mellitus. Expert Rev Proteomics 2018; 16:105-115. [DOI: 10.1080/14789450.2018.1551134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Roel Tans
- Translational Metabolic Laboratory, Department of Laboratory Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lars Verschuren
- Department of Microbiology and Systems Biology, TNO, Zeist, The Netherlands
| | - Hans J. C. T. Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stephan J. L. Bakker
- Department of Internal Medicine, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Cees J. Tack
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jolein Gloerich
- Translational Metabolic Laboratory, Department of Laboratory Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alain J. van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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80
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Yuan H, Jiang B, Zhao B, Zhang L, Zhang Y. Recent Advances in Multidimensional Separation for Proteome Analysis. Anal Chem 2018; 91:264-276. [DOI: 10.1021/acs.analchem.8b04894] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Bo Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Baofeng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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81
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Calderón-Celis F, Encinar JR, Sanz-Medel A. Standardization approaches in absolute quantitative proteomics with mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:715-737. [PMID: 28758227 DOI: 10.1002/mas.21542] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 05/10/2023]
Abstract
Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers. However, the physico-chemical environment of the analyte species affects strongly the ionization efficiency in most mass spectrometry (MS) types, which thereby require the use of specially designed standardization approaches to provide absolute quantifications. Most common of such approaches nowadays include (i) the use of stable isotope-labeled peptide standards, isotopologues to the target proteotypic peptides expected after tryptic digestion of the target protein; (ii) use of stable isotope-labeled protein standards to compensate for sample preparation, sample loss, and proteolysis steps; (iii) isobaric reagents, which after fragmentation in the MS/MS analysis provide a final detectable mass shift, can be used to tag both analyte and standard samples; (iv) label-free approaches in which the absolute quantitative data are not obtained through the use of any kind of labeling, but from computational normalization of the raw data and adequate standards; (v) elemental mass spectrometry-based workflows able to provide directly absolute quantification of peptides/proteins that contain an ICP-detectable element. A critical insight from the Analytical Chemistry perspective of the different standardization approaches and their combinations used so far for absolute quantitative MS-based (molecular and elemental) proteomics is provided in this review.
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Affiliation(s)
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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82
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Krzyszczyk P, Acevedo A, Davidoff EJ, Timmins LM, Marrero-Berrios I, Patel M, White C, Lowe C, Sherba JJ, Hartmanshenn C, O'Neill KM, Balter ML, Fritz ZR, Androulakis IP, Schloss RS, Yarmush ML. The growing role of precision and personalized medicine for cancer treatment. TECHNOLOGY 2018; 6:79-100. [PMID: 30713991 PMCID: PMC6352312 DOI: 10.1142/s2339547818300020] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cancer is a devastating disease that takes the lives of hundreds of thousands of people every year. Due to disease heterogeneity, standard treatments, such as chemotherapy or radiation, are effective in only a subset of the patient population. Tumors can have different underlying genetic causes and may express different proteins in one patient versus another. This inherent variability of cancer lends itself to the growing field of precision and personalized medicine (PPM). There are many ongoing efforts to acquire PPM data in order to characterize molecular differences between tumors. Some PPM products are already available to link these differences to an effective drug. It is clear that PPM cancer treatments can result in immense patient benefits, and companies and regulatory agencies have begun to recognize this. However, broader changes to the healthcare and insurance systems must be addressed if PPM is to become part of standard cancer care.
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Affiliation(s)
- Paulina Krzyszczyk
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Alison Acevedo
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Erika J Davidoff
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Lauren M Timmins
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Ileana Marrero-Berrios
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Misaal Patel
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Corina White
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Christopher Lowe
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Joseph J Sherba
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Clara Hartmanshenn
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ 08854, USA
| | - Kate M O'Neill
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Max L Balter
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Zachary R Fritz
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Ioannis P Androulakis
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ 08854, USA
| | - Rene S Schloss
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, NJ 08854, USA
- Department of Chemical & Biochemical Engineering, Rutgers University, 98 Brett Road, Piscataway, NJ 08854, USA
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83
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Jedinak A, Loughlin KR, Moses MA. Approaches to the discovery of non-invasive urinary biomarkers of prostate cancer. Oncotarget 2018; 9:32534-32550. [PMID: 30197761 PMCID: PMC6126692 DOI: 10.18632/oncotarget.25946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/23/2018] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) continues to be one of the most common cancers in men worldwide. Prostate specific antigen (PSA) measured in blood has been used for decades as an aid for physicians to detect the presence of prostate cancer. However, the PSA test has limited sensitivity and specificity, leading to unnecessary biopsies, overdiagnosis and overtreatment of patients. For these reasons, there is an urgent need for more accurate PCa biomarkers that can detect PCa with high sensitivity and specificity. Urine is a unique source of potential protein biomarkers that can be measured in a non-invasive way. This review comprehensively summarizes state of the art approaches used in the discovery and validation of urinary biomarkers for PCa. Numerous strategies are currently being used in the discovery of urinary biomarkers for prostate cancer including gel-based separation techniques, mass spectrometry, activity-based proteomic assays and software approaches. Antibody-based approaches remain preferred method for validation of candidate biomarkers with rapidly advancing multiplex immunoassays and MS-based targeted approaches. In the last decade, there has been a dramatic acceleration in the development of new techniques and approaches in the discovery of protein biomarkers for prostate cancer including computational, statistical and data mining methods. Many urinary-based protein biomarkers have been identified and have shown significant promise in initial studies. Examples of these potential biomarkers and the methods utilized in their discovery are also discussed in this review.
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Affiliation(s)
- Andrej Jedinak
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Kevin R Loughlin
- Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marsha A Moses
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
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84
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Greco V, Piras C, Pieroni L, Ronci M, Putignani L, Roncada P, Urbani A. Applications of MALDI-TOF mass spectrometry in clinical proteomics. Expert Rev Proteomics 2018; 15:683-696. [PMID: 30058389 DOI: 10.1080/14789450.2018.1505510] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics. Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD). Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.
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Affiliation(s)
- Viviana Greco
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
| | - Cristian Piras
- c Dipartimento di Medicina Veterinaria , Università degli studi di Milano , Milano , Italy
| | - Luisa Pieroni
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy
| | - Maurizio Ronci
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy.,e Department of Medical, Oral and Biotechnological Sciences , University "G. D'Annunzio" of Chieti-Pescara , Chieti , Italy
| | - Lorenza Putignani
- f Unit of Parasitology Bambino Gesù Children's Hospital , IRCCS , Rome , Italy.,g Unit of Human Microbiome , Bambino Gesù Children's Hospital, IRCCS , Rome , Italy
| | - Paola Roncada
- h Dipartimento di Scienze della Salute , Università degli studi "Magna Græcia" di Catanzaro , Catanzaro , Italy
| | - Andrea Urbani
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
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85
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Cai W, Hite ZL, Lyu B, Wu Z, Lin Z, Gregorich ZR, Messer AE, McIlwain SJ, Marston SB, Kohmoto T, Ge Y. Temperature-sensitive sarcomeric protein post-translational modifications revealed by top-down proteomics. J Mol Cell Cardiol 2018; 122:11-22. [PMID: 30048711 DOI: 10.1016/j.yjmcc.2018.07.247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/11/2018] [Accepted: 07/21/2018] [Indexed: 10/28/2022]
Abstract
Despite advancements in symptom management for heart failure (HF), this devastating clinical syndrome remains the leading cause of death in the developed world. Studies using animal models have greatly advanced our understanding of the molecular mechanisms underlying HF; however, differences in cardiac physiology and the manifestation of HF between animals, particularly rodents, and humans necessitates the direct interrogation of human heart tissue samples. Nevertheless, an ever-present concern when examining human heart tissue samples is the potential for artefactual changes related to temperature changes during tissue shipment or sample processing. Herein, we examined the effects of temperature on the post-translational modifications (PTMs) of sarcomeric proteins, the proteins responsible for muscle contraction, under conditions mimicking those that might occur during tissue shipment or sample processing. Using a powerful top-down proteomics method, we found that sarcomeric protein PTMs were differentially affected by temperature. Specifically, cardiac troponin I and enigma homolog isoform 2 showed robust increases in phosphorylation when tissue was incubated at either 4 °C or 22 °C. The observed increase is likely due to increased cyclic AMP levels and activation of protein kinase A in the tissue. On the contrary, cardiac troponin T and myosin regulatory light chain phosphorylation decreased when tissue was incubated at 4 °C or 22 °C. Furthermore, significant protein degradation was also observed after incubation at 4 °C or 22 °C. Overall, these results indicate that temperature exerts various effects on sarcomeric protein PTMs and careful tissue handling is critical for studies involving human heart samples. Moreover, these findings highlight the power of top-down proteomics for examining the integrity of cardiac tissue samples.
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Affiliation(s)
- Wenxuan Cai
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachary L Hite
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Beini Lyu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew E Messer
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Steve B Marston
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Takushi Kohmoto
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Ge
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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86
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dos Santos Seckler H, Fornelli L, Mutharasan RK, Thaxton CS, Fellers R, Daviglus M, Sniderman A, Rader D, Kelleher NL, Lloyd-Jones DM, Compton PD, Wilkins JT. A Targeted, Differential Top-Down Proteomic Methodology for Comparison of ApoA-I Proteoforms in Individuals with High and Low HDL Efflux Capacity. J Proteome Res 2018; 17:2156-2164. [PMID: 29649363 PMCID: PMC6162093 DOI: 10.1021/acs.jproteome.8b00100] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Top-down proteomics (TDP) allows precise determination/characterization of the different proteoforms derived from the expression of a single gene. In this study, we targeted apolipoprotein A-I (ApoA-I), a mediator of high-density-lipoprotein cholesterol efflux (HDL-E), which is inversely associated with coronary heart disease risk. Absolute ApoA-I concentration and allelic variation only partially explain interindividual HDL-E variation. Therefore, we hypothesize that differences in HDL-E are associated with the abundances of different ApoA-I proteoforms. Here, we present a targeted TDP methodology to characterize ApoA-I proteoforms in serum samples and compare their abundances between individuals. We characterized 18 ApoA-I proteoforms using selected-ion monitoring coupled to electron-transfer dissociation mass spectrometry. We then compared the abundances of these proteoforms between two groups of four participants, representing the individuals with highest and lowest HDL-E values within the Chicago Healthy Aging Study ( n = 420). Six proteoforms showed significantly ( p < 0.0005) higher intensity in high HDL-E individuals: canonical ApoA-I [fold difference (fd) = 1.17], carboxymethylated ApoA-I (fd = 1.24) and, with highest difference, four fatty acylated forms: palmitoylated (fd = 2.16), oleoylated (fd = 2.08), arachidonoylated (fd = 2.31) and one bearing two modifications: palmitoylation and truncation (fd = 2.13). These results demonstrate translational potential for targeted TDP in revealing, with high sensitivity, associations between interindividual proteoform variation and physiological differences underlying disease risk.
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Affiliation(s)
- Henrique dos Santos Seckler
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - R. Kannan Mutharasan
- Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Chicago, IL, USA; The Department of Medicine (Cardiology), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - C. Shad Thaxton
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- International Institute for Nanotechnology (IIN), Northwestern University, Evanston, IL, USA
- Feinberg School of Medicine, Department of Urology, Northwestern University, Chicago, IL, USA
| | - Ryan Fellers
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Martha Daviglus
- Northwestern University Feinberg School of Medicine, Department of Preventive Medicine, Chicago, IL, USA
- University of Illinois at Chicago, Institute for Minority Health Research, Chicago, IL, USA
| | - Allan Sniderman
- Royal Victoria Hospital–McGill University Health Centre, Montreal, QC, Canada
| | - Daniel Rader
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Donald M. Lloyd-Jones
- Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Chicago, IL, USA; The Department of Medicine (Cardiology), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern University Feinberg School of Medicine, Department of Preventive Medicine, Chicago, IL, USA
| | - Philip D. Compton
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - John T. Wilkins
- Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Chicago, IL, USA; The Department of Medicine (Cardiology), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern University Feinberg School of Medicine, Department of Preventive Medicine, Chicago, IL, USA
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87
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Lin Z, Guo F, Gregorich ZR, Sun R, Zhang H, Hu Y, Shanmuganayagam D, Ge Y. Comprehensive Characterization of Swine Cardiac Troponin T Proteoforms by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1284-1294. [PMID: 29633223 PMCID: PMC6109964 DOI: 10.1007/s13361-018-1925-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 05/12/2023]
Abstract
Cardiac troponin T (cTnT) regulates the Ca2+-mediated interaction between myosin thick filaments and actin thin filaments during cardiac contraction and relaxation. cTnT is released into the blood following injury, and increased serum levels of the protein are used clinically as a biomarker for myocardial infarction. Moreover, mutations in cTnT are causative in a number of familial cardiomyopathies. With the increasing use of large animal (swine) model to recapitulate human diseases, it is essential to characterize species-dependent protein sequence variants, alternative RNA splicing, and post-translational modifications (PTMs), but challenges remain due to the incomplete database and lack of validation of the predicted splicing isoforms. Herein, we integrated top-down mass spectrometry (MS) with online liquid chromatography (LC) and immunoaffinity purification to comprehensively characterize miniature swine cTnT proteoforms, including those arising from alternative RNA splicing and PTMs. A total of seven alternative splicing isoforms of cTnT were identified by LC/MS from swine left ventricular tissue, with each isoform containing un-phosphorylated and mono-phosphorylated proteoforms. The phosphorylation site was localized to Ser1 for the mono-phosphorylated proteoforms of cTnT1, 3, 4, and 6 by online MS/MS combining collisionally activated dissociation (CAD) and electron transfer dissociation (ETD). Offline MS/MS on Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer with CAD and electron capture dissociation (ECD) was then utilized to achieve deep sequencing of mono-phosphorylated cTnT1 (35.2 kDa) with a high sequence coverage of 87%. Taken together, this study demonstrated the unique advantage of top-down MS in the comprehensive characterization of protein alternative splicing isoforms together with PTMs. Graphical Abstract ᅟ.
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Affiliation(s)
- Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Fang Guo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Cardiology, Shandong Provincial Hospital, Jinan, 250021, Shandong, People's Republic of China
| | - Zachery R Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ruixiang Sun
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
| | - Han Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yang Hu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Chiarini A, Onorati F, Marconi M, Pasquali A, Patuzzo C, Malashicheva A, Irtyega O, Faggian G, Pignatti PF, Trabetti E, Armato U, Dal Pra I. Studies on sporadic non-syndromic thoracic aortic aneurysms: 1. Deregulation of Jagged/Notch 1 homeostasis and selection of synthetic/secretor phenotype smooth muscle cells. Eur J Prev Cardiol 2018; 25:42-50. [DOI: 10.1177/2047487318759119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background Sporadic non-syndromic thoracic aortic aneurysms (SNSTAAs) are less well understood than familial non-syndromic or syndromic ones. The study aimed at defining the peculiar morphologic and molecular changes occurring in the media layer of SNSTAAs. Design This study was based on a single centre design. Methods Media layer samples taken from seven carefully selected SNSTAAs and seven reference patients (controls) were investigated via quantitative polymerase chain reaction, proteomics-bioinformatics, immunoblotting, quantitative histology, and immunohistochemistry/immunofluorescence. Results In SNSTAAs media, aortic smooth muscle cells numbers were halved due to an apoptotic process coupled with a negligible cell proliferation. Cystathionine γ-lyase was diffusely up-regulated. Surviving aortic smooth muscle cells exhibited diverging phenotypes: in inner- and outer-media contractile cells prevailed, having higher contents of smooth-muscle-α-actin holoprotein (45-kDa) and of caspase-3-cleaved smooth-muscle-α-actin 25-kDa fragments; in mid-media, aortic smooth muscle cells exhibited a synthetic/secretor phenotype, down-regulating vimentin, but up-regulating glial fibrillary acidic protein, trans-Golgi network 46 protein, Jagged1 (172-kDa) holoprotein, and Jagged1’s receptor Notch1. Extracellular soluble Jagged1 (42-kDa) fragments accumulated. Conclusions In SNSTAAs, there is a relentless aortic smooth muscle cells attrition caused by the up-regulated cystathionine γ-lyase. In mid-media, synthetic/secretor aortic smooth muscle cells intensify Jagged1/NOTCH1 signalling in the attempt to counterbalance the weakened aortic wall, due to aortic smooth muscle cells net loss and mechanical stress. Synthetic/secretor aortic smooth muscle cells are apoptosis-prone, and the accruing thrombin-cleaved Jagged1 fragments counteract the otherwise useful effects of Jagged1/NOTCH1 signalling, thus hampering tissue homeostasis/remodelling, and aortic smooth muscle cells adhesion, differentiation, and migration.
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Affiliation(s)
- Anna Chiarini
- Histology and Embryology Section, University of Verona Medical School, Italy
| | - Francesco Onorati
- Department of Surgical Sciences, University of Verona Medical School, Italy
| | - Maddalena Marconi
- Histology and Embryology Section, University of Verona Medical School, Italy
| | | | - Cristina Patuzzo
- Biology and Genetics Section, University of Verona Medical School, Italy
| | | | - Olga Irtyega
- Federal Almazov Medical Research Centre, St. Petersburg, Russia
| | - Giuseppe Faggian
- Department of Surgical Sciences, University of Verona Medical School, Italy
| | - Pier F Pignatti
- Biology and Genetics Section, University of Verona Medical School, Italy
| | | | - Ubaldo Armato
- Histology and Embryology Section, University of Verona Medical School, Italy
| | - Ilaria Dal Pra
- Histology and Embryology Section, University of Verona Medical School, Italy
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89
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Naß J, Efferth T. Insights into apoptotic proteins in chemotherapy: quantification techniques and informing therapy choice. Expert Rev Proteomics 2018; 15:413-429. [DOI: 10.1080/14789450.2018.1468755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Janine Naß
- Department of Pharmaceutical Biology, Institute of Biochemistry and Pharmacy, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Biochemistry and Pharmacy, Johannes Gutenberg University, Mainz, Germany
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90
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Salamanca D, Gómez-Chaparro JL, Hidalgo A, Labella F. Differential expression of proteome in aqueous humor in patients with and without glaucoma. ARCHIVOS DE LA SOCIEDAD ESPANOLA DE OFTALMOLOGIA 2018; 93:160-168. [PMID: 29439810 DOI: 10.1016/j.oftal.2017.12.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/20/2017] [Accepted: 12/06/2017] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To determine quantitative and qualitative differences of aqueous humor proteome in patients with and without glaucoma. METHOD Observational, descriptive and cross-sectional study of 12 patients (8 men; 4 women) with and without glaucoma. There are 3 groups of minority proteins with serum equimolar contribution of each of the patients. Specimens were obtained during cataract surgery from patients without glaucoma (performed with retrobulbar anaesthesia [cataract retrobulbar patient -CRP-;n=4] or topical [cataract topical patient -CTP-; n=4]), or from patients with glaucoma (performed with retrobulbar anaesthesia [glaucoma retrobulbar patient -GRP-; n=4]). The humor proteome samples were frozen at -80°C until processing by trypsin digestion to obtain tryptic peptides, and then performing liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) to obtain the proteome and its differential expression between groups. Statistical analysis was performed using the SPSS v.17 program. RESULTS The study included 12 patients, aged (mean±standard deviation) 74.50±9.53 years. Concentrations obtained: 0.48±0.25μg/μl for CRP, 0.28±0.04μg/μl for CTP, and 0.35±0.16μg/μl for GRP. A total of 309 proteins were identified, of which 205, 210, and 182 were in CRP, CTP, and GRP, respectively. A total of 114 proteins were common to all three groups, 50 were exclusive to CRP, 58 to CTP, and 27 to GRP. CONCLUSIONS In this pilot study, a quantitative difference was found in the protein expression of humor among patients with glaucoma, there being 27 proteins unique to patients with glaucomatous disease.
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Affiliation(s)
- D Salamanca
- Universidad de Córdoba (UCO), Córdoba, España.
| | - J L Gómez-Chaparro
- Distrito Córdoba-Guadalquivir (SAS), Córdoba, España; Instituto de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, España
| | - A Hidalgo
- Departamento de Neuro-Oftalmología, Uveítis, Inmunología y Glaucoma, Hospital La Arruzafa, Córdoba, España
| | - F Labella
- Universidad de Córdoba (UCO), Córdoba, España
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91
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Wang Z, Ma H, Smith K, Wu S. Two-Dimensional Separation Using High-pH and Low-pH Reversed Phase Liquid Chromatography for Top-down Proteomics. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:43-51. [PMID: 31097918 PMCID: PMC6516780 DOI: 10.1016/j.ijms.2017.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Advancements in chromatographic separation are critical to in-depth top-down proteomics of complex intact protein samples. Reversed-phase liquid chromatography is the most prevalent technique for top-down proteomics. However, in cases of high complexities and large dynamic ranges, 1D-RPLC may not provide sufficient coverage of the proteome. To address these challenges, orthogonal separation techniques are often combined to improve the coverage and the dynamic range of detection. In this study, a "salt-free" high-pH RPLC was evaluated as an orthogonal dimension of separation to conventional low-pH RPLC with top-down MS. The RPLC separations with low-pH conditions (pH=2) and high-pH conditions (pH=10) were compared to confirm the good orthogonality between high-pH and low-pH RPLC's. The offline 2D RPLC-RPLC-MS/MS analyses of intact E. coli samples were evaluated for the improvement of intact protein identifications as well as intact proteoform characterizations. Compared to the 163 proteins and 328 proteoforms identified using a 1D RPLC-MS approach, 365 proteins and 886 proteoforms were identified using the 2D RPLC-RPLC top-down MS approach. Our results demonstrate that the 2D RPLC-RPLC top-down approach holds great potential for in-depth top-down proteomics studies by utilizing the high resolving power of RPLC separations and by using mass spectrometry compatible buffers for easy sample handling for online MS analysis.
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Affiliation(s)
- Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
| | - Hongyan Ma
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
| | - Kenneth Smith
- Arthritis & Clinical Immunology Research Program, Oklahoma
Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, OK 73104
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma,
101 Stephenson Parkway, Norman, OK 73019
- To whom correspondence should be addressed: Si
Wu, Ph.D., Department of Chemistry and Biochemistry, 101 Stephenson
Parkway, Room 2210, Norman, Oklahoma 73019-5251, United States, Phone: (405)
325-6931, , Fax: (405) 325-6111
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92
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Kachuk C, Doucette AA. The benefits (and misfortunes) of SDS in top-down proteomics. J Proteomics 2018; 175:75-86. [DOI: 10.1016/j.jprot.2017.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/19/2017] [Accepted: 03/03/2017] [Indexed: 12/18/2022]
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93
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Schmit PO, Vialaret J, Wessels HJ, van Gool AJ, Lehmann S, Gabelle A, Wood J, Bern M, Paape R, Suckau D, Kruppa G, Hirtz C. Towards a routine application of Top-Down approaches for label-free discovery workflows. J Proteomics 2018; 175:12-26. [DOI: 10.1016/j.jprot.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
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94
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Pawlowski JW, Carrick I, Kaltashov IA. Integration of On-Column Chemical Reactions in Protein Characterization by Liquid Chromatography/Mass Spectrometry: Cross-Path Reactive Chromatography. Anal Chem 2018; 90:1348-1355. [DOI: 10.1021/acs.analchem.7b04328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jake W. Pawlowski
- Department of Chemistry, University of Massachusetts—Amherst, Amherst, Massachusetts 01003, United States
| | - Ian Carrick
- Department of Chemistry, University of Massachusetts—Amherst, Amherst, Massachusetts 01003, United States
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts—Amherst, Amherst, Massachusetts 01003, United States
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95
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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96
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Laputková G, Schwartzová V, Bánovčin J, Alexovič M, Sabo J. Salivary Protein Roles in Oral Health and as Predictors of Caries Risk. Open Life Sci 2018; 13:174-200. [PMID: 33817083 PMCID: PMC7874700 DOI: 10.1515/biol-2018-0023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022] Open
Abstract
This work describes the current state of research on the potential relationship between protein content in human saliva and dental caries, which remains among the most common oral diseases and causes irreversible damage in the oral cavity. An understanding the whole saliva proteome in the oral cavity could serve as a prerequisite to obtaining insight into the etiology of tooth decay at early stages. To date, however, there is no comprehensive evidence showing that salivary proteins could serve as potential indicators for the early diagnosis of the risk factors causing dental caries. Therefore, proteomics indicates the promising direction of future investigations of such factors, including diagnosis and thus prevention in dental therapy.
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Affiliation(s)
- Galina Laputková
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
| | - Vladimíra Schwartzová
- 1st Department of Stomatology, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
| | - Juraj Bánovčin
- Department of Stomatology and Maxillofacial Surgery, Faculty of Medicine, University of P. J. Šafárik in Košice, Rastislavova 43, Košice, 041 90, Slovakia
| | - Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P. J. Šafárik in Košice, Trieda SNP 1, Košice, 040 11, Slovakia
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97
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Riley NM, Westphall MS, Coon JJ. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:140-149. [PMID: 29027149 PMCID: PMC5786479 DOI: 10.1007/s13361-017-1808-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/31/2017] [Accepted: 09/02/2017] [Indexed: 05/12/2023]
Abstract
The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (<30 kDa). Recent studies have focused on improving the analysis of larger intact proteins (up to ~75 kDa), but they have also highlighted several challenges to be addressed. One major hurdle is the efficient dissociation of larger protein ions, which often to do not yield extensive fragmentation via conventional tandem MS methods. Here we describe the first application of activated ion electron transfer dissociation (AI-ETD) to proteins in the 30-70 kDa range. AI-ETD leverages infrared photo-activation concurrent to ETD reactions to improve sequence-informative product ion generation. This method generates more product ions and greater sequence coverage than conventional ETD, higher-energy collisional dissociation (HCD), and ETD combined with supplemental HCD activation (EThcD). Importantly, AI-ETD provides the most thorough protein characterization for every precursor ion charge state investigated in this study, making it suitable as a universal fragmentation method in top-down experiments. Additionally, we highlight several acquisition strategies that can benefit characterization of larger proteins with AI-ETD, including combination of spectra from multiple ETD reaction times for a given precursor ion, multiple spectral acquisitions of the same precursor ion, and combination of spectra from two different dissociation methods (e.g., AI-ETD and HCD). In all, AI-ETD shows great promise as a method for dissociating larger intact protein ions as top-down proteomics continues to advance into larger mass ranges. Graphical Abstract ᅟ.
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Affiliation(s)
- Nicholas M Riley
- Genome Center of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Joshua J Coon
- Genome Center of Wisconsin, Madison, WI, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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98
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Peng L, Cantor DI, Huang C, Wang K, Baker MS, Nice EC. Tissue and plasma proteomics for early stage cancer detection. Mol Omics 2018; 14:405-423. [PMID: 30251724 DOI: 10.1039/c8mo00126j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The pursuit of novel and effective biomarkers is essential in the struggle against cancer, which is a leading cause of mortality worldwide. Here we discuss the relative advantages and disadvantages of the most frequently used proteomics techniques, concentrating on the latest advances and application of tissue and plasma proteomics for novel cancer biomarker discovery.
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Affiliation(s)
- Liyuan Peng
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - David I. Cantor
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Macquarie University
- New South Wales
- Australia
| | - Canhua Huang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Kui Wang
- Dept of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy
- Chengdu
- P. R. China
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University
- Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University
- Clayton
- Australia
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99
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Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM. Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Anal Chem 2017; 90:1325-1333. [PMID: 29227670 DOI: 10.1021/acs.analchem.7b04221] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In top-down proteomics, intact proteins are analyzed by tandem mass spectrometry and proteoforms, which are defined forms of a protein with specific sequences of amino acids and localized post-translational modifications, are identified using precursor mass and fragmentation data. Many proteoforms that are detected in the precursor scan (MS1) are not selected for fragmentation by the instrument and therefore remain unidentified in typical top-down proteomic workflows. Our laboratory has developed the open source software program Proteoform Suite to analyze MS1-only intact proteoform data. Here, we have adapted it to provide identifications of proteoform masses in precursor MS1 spectra of top-down data, supplementing the top-down identifications obtained using the MS2 fragmentation data. Proteoform Suite performs mass calibration using high-scoring top-down identifications and identifies additional proteoforms using calibrated, accurate intact masses. Proteoform families, the set of proteoforms from a given gene, are constructed and visualized from proteoforms identified by both top-down and intact-mass analyses. Using this strategy, we constructed proteoform families and identified 1861 proteoforms in yeast lysate, yielding an approximately 40% increase over the original 1291 proteoform identifications observed using traditional top-down analysis alone.
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Affiliation(s)
- Leah V Schaffer
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Brian L Frey
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Stefan K Solntsev
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.,Genome Center of Wisconsin, University of Wisconsin , 425G Henry Mall, Room 3420, Madison, Wisconsin 53706, United States
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100
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Soboleva A, Schmidt R, Vikhnina M, Grishina T, Frolov A. Maillard Proteomics: Opening New Pages. Int J Mol Sci 2017; 18:E2677. [PMID: 29231845 PMCID: PMC5751279 DOI: 10.3390/ijms18122677] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/29/2017] [Accepted: 12/05/2017] [Indexed: 12/12/2022] Open
Abstract
Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs) represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer's disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus), proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.
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Affiliation(s)
- Alena Soboleva
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Rico Schmidt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther Universität Halle-Wittenberg, 06108 Halle, Germany.
| | - Maria Vikhnina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Tatiana Grishina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
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