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Thongboonkerd V, Chaiyarit S. Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins. Curr Protoc 2022; 2:e390. [PMID: 35275445 DOI: 10.1002/cpz1.390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitochondrion is a key intracellular organelle regulating metabolic processes, oxidative stress, energy production, calcium homeostasis, and cell survival. Protein phosphorylation plays an important role in regulating mitochondrial functions and cellular signaling pathways. Dysregulation of protein phosphorylation status can cause protein malfunction and abnormal signal transduction, leading to organ dysfunction and disease. Investigating the mitochondrial phosphoproteins is therefore crucial to better understand the molecular and pathogenic mechanisms of many metabolic disorders. Conventional analyses of phosphoproteins, for instance, via western blotting, can be done only for proteins for which specific antibodies to their phosphorylated forms are available. Moreover, such an approach is not suitable for large-scale study of phosphoproteins. Currently, proteomics represents an important tool for large-scale analysis of proteins and their post-translational modifications, including phosphorylation. Here, we provide step-by-step protocols for the proteomics analysis of mitochondrial phosphoproteins (the phosphoproteome), using renal tubular cells as an example. These protocols include methods to effectively isolate mitochondria and to validate the efficacy of mitochondrial enrichment as well as its purity. We also provide detailed protocols for performing both gel-based and gel-free phosphoproteome analyses. The gel-based analysis involves two-dimensional gel electrophoresis and phosphoprotein-specific staining, followed by protein identification via mass spectrometry, whereas the gel-free approach is based on in-solution mass spectrometric identification of specific phosphorylation sites and residues. In all, these approaches allow large-scale analyses of mitochondrial phosphoproteins that can be applied to other cells and tissues of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Mitochondrial isolation/purification from renal tubular cells Support Protocol: Validation of enrichment efficacy and purity of mitochondrial isolation Basic Protocol 2: Gel-based phosphoproteome analysis Basic Protocol 3: Gel-free phosphoproteome analysis.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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2
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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3
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Dimethyl Labeling-Based Quantitative Proteomics of Recalcitrant Cocoa Pod Tissue. Methods Mol Biol 2020. [PMID: 32462583 DOI: 10.1007/978-1-0716-0528-8_10] [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
Dimethyl labeling is a type of stable-isotope labeling suitable for creating isotopic variants of peptides and thus be utilized for quantitative proteomics experiments. Labeling is achieved through a reductive amination/alkylation reaction using the low-cost reagents formaldehyde and cyanoborohydride, resulting in dimethylation of free amine groups of Lys and N-termini. Availability of isotopomeric forms of these reagents allows for the generation of up to six different isotopic variants. Here we describe the application of dimethylation to create two isotopic variants, light and heavy, differing in 4 Da, to label the total tryptic digest peptides of cocoa pod extracted from healthy pods from cultivars susceptible and resistant to the fungal disease called "frosty pod" caused by Moniliophthora roreri.
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4
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Choi Y, Jeong K, Shin S, Lee JW, Lee YS, Kim S, Kim SA, Jung J, Kim KP, Kim VN, Kim JS. MS1-Level Proteome Quantification Platform Allowing Maximally Increased Multiplexity for SILAC and In Vitro Chemical Labeling. Anal Chem 2020; 92:4980-4989. [PMID: 32167278 DOI: 10.1021/acs.analchem.9b05148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quantitative proteomic platforms based on precursor intensity in mass spectrometry (MS1-level) uniquely support in vivo metabolic labeling with superior quantification accuracy but suffer from limited multiplexity (≤3-plex) and frequent missing quantities. Here we present a new MS1-level quantification platform that allows maximal multiplexing with high quantification accuracy and precision for the given labeling scheme. The platform currently comprises 6-plex in vivo SILAC or in vitro diethylation labeling with a dedicated algorithm and is also expandable to higher multiplexity (e.g., nine-plex for SILAC). For complex samples with broad dynamic ranges such as total cell lysates, our platform performs highly accurately and free of missing quantities. Furthermore, we successfully applied our method to measure protein synthesis rate under heat shock response in human cells by 6-plex pulsed SILAC experiments, demonstrating the unique biological merits of our in vivo platform to disclose translational regulations for cellular response to stress.
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Affiliation(s)
- Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kyowon Jeong
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Joon Won Lee
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Sangtae Kim
- Illumina, Inc., San Diego, California 92122, United States
| | - Sun Ah Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jaehun Jung
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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Zhang S, Yuan H, Zhao B, Zhang L, Zhang Y. Integrated platform with combination of on-line protein digestion, isotope dimethyl labeling and multidimensional peptide separation for high-throughput proteome quantification. Anal Chim Acta 2018; 1000:172-179. [DOI: 10.1016/j.aca.2017.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 02/08/2023]
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Rudolph JD, de Graauw M, van de Water B, Geiger T, Sharan R. Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks. Cell Syst 2016; 3:585-593.e3. [DOI: 10.1016/j.cels.2016.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/24/2016] [Accepted: 11/09/2016] [Indexed: 01/01/2023]
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7
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Hsu JL, Chen SH. Stable isotope dimethyl labelling for quantitative proteomics and beyond. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0364. [PMID: 27644970 PMCID: PMC5031631 DOI: 10.1098/rsta.2015.0364] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 05/21/2023]
Abstract
Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jue-Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan City, Taiwan, Republic of China
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Lv X, Tan W, Chen Y, Chen Y, Ma M, Chen B, Yao S. Facile “one-pot” synthesis of poly(methacrylic acid)-based hybrid monolith via thiol-ene click reaction for hydrophilic interaction chromatography. J Chromatogr A 2016; 1454:49-57. [DOI: 10.1016/j.chroma.2016.05.072] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/18/2016] [Accepted: 05/22/2016] [Indexed: 01/24/2023]
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Lochmatter C, Fischer R, Charles PD, Yu Z, Powrie F, Kessler BM. Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes. Sci Rep 2016; 6:24491. [PMID: 27080861 PMCID: PMC4832251 DOI: 10.1038/srep24491] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/30/2016] [Indexed: 12/15/2022] Open
Abstract
Interleukin (IL)-23 mediated signal transduction represents a major molecular mechanism underlying the pathology of inflammatory bowel disease, Crohn's disease and ulcerative colitis. In addition, emerging evidence supports the role of IL-23-driven Th17 cells in inflammation. Components of the IL-23 signaling pathway, such as IL-23R, JAK2 and STAT3, have been characterized, but elements unique to this network as compared to other interleukins have not been readily explored. In this study, we have undertaken an integrative phosphoproteomics approach to better characterise downstream signaling events. To this end, we performed and compared phosphopeptide and phosphoprotein enrichment methodologies after activation of T lymphocytes by IL-23. We demonstrate the complementary nature of the two phosphoenrichment approaches by maximizing the capture of phosphorylation events. A total of 8202 unique phosphopeptides, and 4317 unique proteins were identified, amongst which STAT3, PKM2, CDK6 and LASP-1 showed induction of specific phosphorylation not readily observed after IL-2 stimulation. Interestingly, quantitative analysis revealed predominant phosphorylation of pre-existing STAT3 nuclear subsets in addition to translocation of phosphorylated STAT3 within 30 min after IL-23 stimulation. After IL-23R activation, a small subset of PKM2 also translocates to the nucleus and may contribute to STAT3 phosphorylation, suggesting multiple cellular responses including metabolic adaptation.
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Affiliation(s)
- Corinne Lochmatter
- Kennedy Institute, Nuffield Department of Orthopedics Research Medical Science, Roosevelt Drive, Oxford OX3 7LF, UK
- Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Roman Fischer
- Kennedy Institute, Nuffield Department of Orthopedics Research Medical Science, Roosevelt Drive, Oxford OX3 7LF, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Philip D. Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Zhanru Yu
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Fiona Powrie
- Kennedy Institute, Nuffield Department of Orthopedics Research Medical Science, Roosevelt Drive, Oxford OX3 7LF, UK
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
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Abstract
OBJECTIVES The aim of this study was to identify differentially expressed proteins among various stages of pancreatic ductal adenocarcinoma (PDAC) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry and stable isotope dimethyl labeling. METHODS Differentially expressed proteins were identified and compared based on the mass spectral differences of their isotope-labeled peptide fragments generated from protease digestion. RESULTS Our quantitative proteomic analysis of the differentially expressed proteins with stable isotope (deuterium/hydrogen ratio, ≥ 2) identified a total of 353 proteins, with at least 5 protein biomarker proteins that were significantly differentially expressed between cancer and normal mice by at least a 2-fold alteration. These 5 protein biomarker candidates include α-enolase, α-catenin, 14-3-3 β, VDAC1, and calmodulin with high confidence levels. The expression levels were also found to be in agreement with those examined by Western blot and histochemical staining. CONCLUSIONS The systematic decrease or increase of these identified marker proteins may potentially reflect the morphological aberrations and diseased stages of pancreas carcinoma throughout progressive developments leading to PDAC. The results would form a firm foundation for future work concerning validation and clinical translation of some identified biomarkers into targeted diagnosis and therapy for various stages of PDAC.
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Bensaddek D, Nicolas A, Lamond AI. Evaluating the use of HILIC in large-scale, multi dimensional proteomics: Horses for courses? INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 391:105-114. [PMID: 26869852 PMCID: PMC4708065 DOI: 10.1016/j.ijms.2015.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/06/2015] [Accepted: 07/28/2015] [Indexed: 06/05/2023]
Abstract
Despite many recent advances in instrumentation, the sheer complexity of biological samples remains a major challenge in large-scale proteomics experiments, reflecting both the large number of protein isoforms and the wide dynamic range of their expression levels. However, while the dynamic range of expression levels for different components of the proteome is estimated to be ∼107-8, the equivalent dynamic range of LC-MS is currently limited to ∼106. Sample pre-fractionation has therefore become routinely used in large-scale proteomics to reduce sample complexity during MS analysis and thus alleviate the problem of ion suppression and undersampling. There is currently a wide range of chromatographic techniques that can be applied as a first dimension separation. Here, we systematically evaluated the use of hydrophilic interaction liquid chromatography (HILIC), in comparison with hSAX, as a first dimension for peptide fractionation in a bottom-up proteomics workflow. The data indicate that in addition to its role as a useful pre-enrichment method for PTM analysis, HILIC can provide a robust, orthogonal and high-resolution method for increasing the depth of proteome coverage in large-scale proteomics experiments. The data also indicate that the choice of using either HILIC, hSAX, or other methods, is best made taking into account the specific types of biological analyses being performed.
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Affiliation(s)
| | | | - Angus I. Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
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12
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Onco-proteogenomics identifies urinary S100A9 and GRN as potential combinatorial biomarkers for early diagnosis of hepatocellular carcinoma. BBA CLINICAL 2015; 3:205-13. [PMID: 26675302 PMCID: PMC4669941 DOI: 10.1016/j.bbacli.2015.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC), the major type of liver cancer, is among the most lethal cancers owing to its aggressive nature and frequently late detection. Therefore, the possibility to identify early diagnostic markers could be of significant benefit. Urine has especially become one of the most attractive body fluids in biomarker discovery as it can be obtained non-invasively in large quantities and is stable as compared with other body fluids. To identify potential protein biomarker for early diagnosis of HCC, we explored protein expression profiles in urine from HCC patients and normal controls (n = 44) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry (nanoLC–MS/MS) and stable isotope dimethyl labeling. We have systematically mapped 91 proteins with differential expressions (p < 0.05), which included 8 down-regulated microtubule proteins and 83 up-regulated proteins involved in signal and inflammation response. Further integrated proteogenomic approach composed of proteomic, genomic and transcriptomic analysis identified that S100A9 and GRN were co-amplified (p < 0.001) and co-expressed (p < 0.01) in HCC tumors and urine samples. In addition, the amplifications of S100A9 or GRN were found to be associated with poor survival in HCC patients, and their co-amplification was also prognosed worse overall survival than individual ones. Our results suggest that urinary S100A9 and GRN as potential combinatorial biomarkers can be applied to early diagnosis of hepatocellular carcinoma and highlight the utility of onco-proteogenomics for identifying protein markers that can be applied to disease-oriented translational medicine. An integrated proteogenomic analysis is applied to identify biomarkers for HCC. Genomic amplifications of S100A9 and GRN co-occur in tumors from HCC patients. S100A9 and GRN are co-expressed in tumor and urine samples from HCC patients. Amplifications of S100A9 and GRN are associated with poor survival of HCC patients.
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Chiou SH, Huang CH, Liang SS. From Chemistry to Translational Medicine: The Application of Proteomics to Cancer Biomarker Discovery and Diagnosis. J CHIN CHEM SOC-TAIP 2015. [DOI: 10.1002/jccs.201400350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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14
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Yang C, Zhong X, Li L. Recent advances in enrichment and separation strategies for mass spectrometry-based phosphoproteomics. Electrophoresis 2014; 35:3418-29. [PMID: 24687451 PMCID: PMC4849134 DOI: 10.1002/elps.201400017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/21/2014] [Accepted: 03/21/2014] [Indexed: 12/29/2022]
Abstract
Due to the significance of protein phosphorylation in various biological processes and signaling events, new analytical techniques for enhanced phosphoproteomics have been rapidly introduced in the recent years. The combinatorial use of the phospho-specific enrichment techniques and prefractionation methods prior to MS analysis enable comprehensive profiling of the phosphoproteome and facilitate deciphering the critical roles that phosphorylation plays in signaling pathways in various biological systems. This review places special emphasis on the recent five-year (2009-2013) advances for enrichment and separation techniques that have been utilized for phosphopeptides prior to MS analysis.
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Affiliation(s)
- Chenxi Yang
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Xuefei Zhong
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- School of Pharmacy, University of Wisconsin, 777 Highland Avenue, Madison, Wisconsin 53705, United States
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Huang J, Wang F, Ye M, Zou H. Enrichment and separation techniques for large-scale proteomics analysis of the protein post-translational modifications. J Chromatogr A 2014; 1372C:1-17. [DOI: 10.1016/j.chroma.2014.10.107] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/16/2022]
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Zhai G, Wu X, Luo Q, Wu K, Zhao Y, Liu J, Xiong S, Feng YQ, Yang L, Wang F. Evaluation of serum phosphopeptides as potential cancer biomarkers by mass spectrometric absolute quantification. Talanta 2014; 125:411-7. [DOI: 10.1016/j.talanta.2014.03.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/25/2023]
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17
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Marchini FK, de Godoy LMF, Batista M, Kugeratski FG, Krieger MA. Towards the phosphoproteome of trypanosomatids. Subcell Biochem 2014; 74:351-378. [PMID: 24264253 DOI: 10.1007/978-94-007-7305-9_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The identification and localization of protein phosphorylation sites provide clues to what proteins or pathways might be activated in a given condition, helping to improve our understanding about signaling networks. Advances in strategies for enrichment of phosphorylated peptides/proteins, mass spectrometry (MS) instrumentation, and specific MS techniques for identification and quantification of post-translational modifications have allowed for large-scale mapping of phosphorylation sites, promoting the field of phosphoproteomics. The great promise of phosphoproteomics is to unravel the dynamics of signaling networks, a layer of the emerging field of systems biology. Until a few years ago only a small number of phosphorylation sites had been described. Following large-scale trends, recent phosphoproteomic studies have reported the mapping of thousands of phosphorylation sites in trypanosomatids. However, quantitative information about the regulation of such sites in different conditions is still lacking. In this chapter, we provide a historical overview of phosphoproteomic studies for trypanosomatids and discuss some challenges and perspectives in the field.
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Dudley E, Bond AE. Phosphoproteomic Techniques and Applications. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:25-69. [DOI: 10.1016/b978-0-12-800453-1.00002-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Fleitz A, Nieves E, Madrid-Aliste C, Fentress SJ, Sibley LD, Weiss LM, Angeletti RH, Che FY. Enhanced detection of multiply phosphorylated peptides and identification of their sites of modification. Anal Chem 2013; 85:8566-76. [PMID: 23889490 PMCID: PMC3841110 DOI: 10.1021/ac401691g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phosphorylation is an important post-translational modification that rapidly mediates many cellular events. A key to understanding the dynamics of the phosphoproteome is localization of the modification site(s), primarily determined using LC-MS/MS. A major technical challenge to analysis is the formation of phosphopeptide-metal ion complexes during LC which hampers phosphopeptide detection. We have devised a strategy that enhances analysis of phosphopeptides, especially multiply phosphorylated peptides. It involves treatment of the LC system with EDTA and 2D-RP/RP-nanoUPLC-MS/MS (high pH/low pH) analysis. A standard triphosphorylated peptide that could not be detected with 1D-RP-nanoUPLC-MS/MS, even if the column was treated with EDTA-Na2 or if 25 mM EDTA-Na2 was added to the sample, was detectable at less than 100 fmol using EDTA-2D-RP/RP-nanoUPLC-MS/MS. Digests of α-casein and ß-casein were analyzed by EDTA-1D-RP-nanoUPLC, 2D-RP/RP-nanoUPLC, and EDTA-2D-RP/RP-nanoUPLC to compare their performance in phosphopeptide analysis. With the first two approaches, no tri- and tetraphosphopeptides were identified in either α- or ß-casein sample. With the EDTA-2D-RP/RP approach, 13 mono-, 6 di-, and 3 triphosphopeptides were identified in the α-casein sample, while 19 mono-, 8 di-, 4 tri-, and 3 tetraphosphopeptides were identified in the ß-casein sample. Using EDTA-2D-RP/RP-nanoUPLC-MS/MS to examine 500 μg of a human foreskin fibroblast cell lysate a total of 1,944 unique phosphopeptides from 1,087 unique phosphoproteins were identified, and 2,164 unique phosphorylation sites were confidently localized (Ascore ≥20). Of these sites 79% were mono-, 20% di-, and ∼1% were tri- and tetraphosphopeptides, and 78 novel phosphorylation sites in human proteins were identified.
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Affiliation(s)
- Antoine Fleitz
- Program in Genomics and Proteomics, University of Lille, France
| | - Edward Nieves
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Carlos Madrid-Aliste
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Sarah J. Fentress
- Department of Molecular Microbiology, Washington University, St. Louis, Missouri 63110, United States
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University, St. Louis, Missouri 63110, United States
| | - Louis M. Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
- Department of Medicine (Infectious Diseases), Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Ruth Hogue Angeletti
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Fa-Yun Che
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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Engholm-Keller K, Larsen MR. Technologies and challenges in large-scale phosphoproteomics. Proteomics 2013; 13:910-31. [PMID: 23404676 DOI: 10.1002/pmic.201200484] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/18/2013] [Accepted: 01/31/2013] [Indexed: 12/23/2022]
Abstract
Phosphorylation, the reversible addition of a phosphate group to amino acid side chains of proteins, is a fundamental regulator of protein activity, stability, and molecular interactions. Most cellular processes, such as inter- and intracellular signaling, protein synthesis, degradation, and apoptosis, rely on phosphorylation. This PTM is thus involved in many diseases, rendering localization and assessment of extent of phosphorylation of major scientific interest. MS-based phosphoproteomics, which aims at describing all phosphorylation sites in a specific type of cell, tissue, or organism, has become the main technique for discovery and characterization of phosphoproteins in a nonhypothesis driven fashion. In this review, we describe methods for state-of-the-art MS-based analysis of protein phosphorylation as well as the strategies employed in large-scale phosphoproteomic experiments with focus on the various challenges and limitations this field currently faces.
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Affiliation(s)
- Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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21
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Kuo CJ, Liang SS, Hsi E, Chiou SH, Lin SD. Quantitative proteomics analysis of varicose veins: identification of a set of differentially expressed proteins related to ATP generation and utilization. Kaohsiung J Med Sci 2013; 29:594-605. [PMID: 24183353 DOI: 10.1016/j.kjms.2013.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/19/2012] [Indexed: 01/12/2023] Open
Abstract
Although morphological and anatomical studies indicate that varicose veins are characterized by venous wall weakening and subendothelial fibrosis, the exact underlying biochemical mechanism of their development remains unknown. Additionally, no quantitative proteomic study of venous proteins leading to decreased contractility of varicose veins has been reported to date. Therefore, to elucidate the molecular mechanism of altered vascular contractility, this study performed shotgun proteomic analysis to obtain protein expression profiles in patients with varicose veins. Stable isotope dimethyl labeling coupled with nanoLC-MS/MS revealed downregulation in 12 polypeptides, including myosin light chain kinase, creatine kinase B-type, ATP synthase, phosphoglycerate kinase, and pyruvate kinase. However, analyses of protein species associated with cytoskeletal assembly or with cellular morphology showed no clear up- or down-regulation. These results indicate that defects in ATP generation and utilization may account for the dysfunction of vascular smooth muscle following formation of varicose veins. Collectively, the severity of varicose veins depends on the regulatory roles of various protein factors in the metabolic coordination of physiological functions. This pilot study improves understanding of the pathogenesis of varicose veins and lays the foundation for further validation and clinical translation of biomarkers for targeted therapies in treating this disease.
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Affiliation(s)
- Chao-Jen Kuo
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Center for Research Resources and Development, Kaohsiung Medical University, Kaohsiung, Taiwan
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22
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D'Attoma A, Heinisch S. On-line comprehensive two dimensional separations of charged compounds using reversed-phase high performance liquid chromatography and hydrophilic interaction chromatography. Part II: application to the separation of peptides. J Chromatogr A 2013; 1306:27-36. [PMID: 23891372 DOI: 10.1016/j.chroma.2013.07.048] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/07/2013] [Accepted: 07/11/2013] [Indexed: 11/16/2022]
Abstract
In this second paper of a two-part series, on-line RPLC×HILIC is compared to on-line RPLC×RPLC through the separation of peptides. Our choices regarding the conditions are discussed. Injection effects and overloading effects are evaluated in both configurations. It is shown that whereas large volumes can be injected in the second dimension in RPLC×RPLC under HT-UHPLC conditions (>20% of the column dead volume), even small injection volumes (8% of the column the dead volume) have a detrimental effect on peak shapes in RPLC×HILIC. Advantages and limits of the two 2D-systems are compared through the 2D-separation of a tryptic digest of three proteins. A ten-fold gain in analysis time along with a significant gain in peak capacity are obtained with both systems compared to the most efficient one-dimensional separation of peptides recently published.
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Affiliation(s)
- Amélie D'Attoma
- Institut des Sciences Analytiques, UMR CNRS 5280, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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23
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Chester TL. Recent Developments in High-Performance Liquid Chromatography Stationary Phases. Anal Chem 2012; 85:579-89. [DOI: 10.1021/ac303180y] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Thomas L. Chester
- Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati,
Ohio 45221-0172, United States
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24
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Sample preparation and analytical strategies for large-scale phosphoproteomics experiments. Semin Cell Dev Biol 2012; 23:843-53. [DOI: 10.1016/j.semcdb.2012.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 05/29/2012] [Indexed: 12/28/2022]
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25
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Sun Z, Hamilton KL, Reardon KF. Phosphoproteomics and molecular cardiology: Techniques, applications and challenges. J Mol Cell Cardiol 2012; 53:354-68. [DOI: 10.1016/j.yjmcc.2012.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 05/26/2012] [Accepted: 06/03/2012] [Indexed: 12/16/2022]
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26
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Becnel LB, McKenna NJ. Minireview: progress and challenges in proteomics data management, sharing, and integration. Mol Endocrinol 2012; 26:1660-74. [PMID: 22902541 DOI: 10.1210/me.2012-1180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The proteome represents the identity, expression levels, interacting partners, and posttranslational modifications of proteins expressed within any given cell. Proteomic studies aim to census the quantitative and qualitative factors regulating the biological relationships of proteins acting in concert as functional cellular networks. In the field of endocrinology, proteomics has been of considerable value in determining the function and mechanism of action of endocrine signaling molecules in the cell membrane, cytoplasm, and nucleus and for the discovery of proteins as candidates for clinical biomarkers. The volume of data that can be generated by proteomics methodologies, up to gigabytes of data within a few hours, brings with it its own logistical hurdles and presents significant challenges to realizing the full potential of these datasets. In this minireview, we describe selected current proteomics methodologies and their application in basic and translational endocrinology before focusing on mass spectrometry as a model for current progress and challenges in data analysis, management, sharing, and integration.
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Affiliation(s)
- Lauren B Becnel
- Department of Medicine, Hematology and Oncology, Baylor College of Medicine, 1 Baylor Plaza MS-BCM305, Houston, Texas 77030, USA.
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27
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Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 2012; 404:939-65. [PMID: 22772140 DOI: 10.1007/s00216-012-6203-4] [Citation(s) in RCA: 539] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/06/2012] [Accepted: 06/15/2012] [Indexed: 02/08/2023]
Abstract
Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.
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Chen CH, Hong JX, Wu CS, Chen SH. Gold nanoparticle-based immuno dual probes for targeting proteomics. J Proteome Res 2012; 11:3921-8. [PMID: 22630171 DOI: 10.1021/pr300315n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Immunoprecipitation combined with mass spectrometry (MS) is a promising technique for targeting proteomics in characterizing submicrograms of target protein and interacting proteins in living cells. This method, however, is limited by interference arising from nonspecific binding. We report a novel gold nanoparticle (AuNP)-based immuno probe approach for immunoprecipitation. By cross-linking the antibody Fc domain to protein G covalently modified on AuNPs, the probe was fabricated and characterized to have 60 protein G and 30 immunoglobins per AuNP. We used human immunoglobin against the target and mouse immunoglobin with the same isotype (IgG) to fabricate the target and preclear probe, respectively, and termed it as the dual probe approach. Our results showed that the preclear probe (AuNP-IgG) and the target probe (AuNP-anti-ERα) share a similar panel of nonspecific binders but dramatic different specificity toward the target. Thus, using the dual probe method, we showed major nonspecific binders in the cell lysate could be largely removed without sacrificing the target protein. Compared to the conventional agarose gel-chromatography, the AuNP-based probe exhibited less nonspecific interference and higher recovery yield for ERα. Moreover, the AuNP-based probe is more inert than the agarose gel under harsh conditions and does not induce dissociation of the cross-linked IgG that could interfere with target identification. Using AuNP-based dual probes, ERα was shown to be purified from MCF-7 cells with minimum nonspecific binding. Moreover, the identity and phosphorylation sites on the C-terminus of the purified ERα could be positively confirmed by MS using only 1 mg of cellular protein.
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Affiliation(s)
- Chan-Hua Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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29
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Di Palma S, Hennrich ML, Heck AJ, Mohammed S. Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis. J Proteomics 2012; 75:3791-813. [DOI: 10.1016/j.jprot.2012.04.033] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/19/2012] [Accepted: 04/23/2012] [Indexed: 10/28/2022]
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30
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Kovanich D, Cappadona S, Raijmakers R, Mohammed S, Scholten A, Heck AJR. Applications of stable isotope dimethyl labeling in quantitative proteomics. Anal Bioanal Chem 2012; 404:991-1009. [DOI: 10.1007/s00216-012-6070-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 04/13/2012] [Accepted: 04/23/2012] [Indexed: 01/03/2023]
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31
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Aye TT, Low TY, Bjørlykke Y, Barsnes H, Heck AJR, Berven FS. Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins. Anal Chem 2012; 84:4999-5006. [PMID: 22548487 DOI: 10.1021/ac300596r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this manuscript, we present a proof-of-concept study for targeted relative protein quantitation workflow using chemical labeling in the form of dimethylation, coupled with selected reaction monitoring (dimethyl-SRM). We first demonstrate close to complete isotope incorporation for all peptides tested. The accuracy, reproducibility, and linear dynamic range of quantitation are further assessed based on known ratios of nonhuman standard proteins spiked into human cerebrospinal fluid (CSF) as a model complex matrix. Quantitation reproducibility below 20% (CV < 20%) was obtained for analyte concentrations present at a dynamic range of 4 orders of magnitude lower than that of the background proteins. An error of less than 15% was observed when measuring the abundance of 44 out of 45 major human plasma proteins. Dimethyl-SRM was further examined by comparing the relative quantitation of eight proteins in human CSF with the relative quantitation obtained using synthetic heavy peptides coupled to stable isotope dilution-SRM (SID-SRM). Comparison between the two methods reveals that the correlation between dimethyl-SRM and SID-SRM is within 0.3-33% variation, demonstrating the accuracy of relative quantitation using dimethyl-SRM. Dimethyl labeling coupled with SRM provides a fast, convenient, and cost-effective alternative for relative quantitation of a large number of candidate proteins/peptides.
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Affiliation(s)
- Thin Thin Aye
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
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32
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Ray BN, Kweon HK, Argetsinger LS, Fingar DC, Andrews PC, Carter-Su C. Research resource: identification of novel growth hormone-regulated phosphorylation sites by quantitative phosphoproteomics. Mol Endocrinol 2012; 26:1056-73. [PMID: 22570334 PMCID: PMC3858665 DOI: 10.1210/me.2011-1258] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
GH and GH receptors are expressed throughout life, and GH elicits a diverse range of responses, including growth and altered metabolism. It is therefore important to understand the full spectrum of GH signaling pathways and cellular responses. We applied mass spectrometry-based phosphoproteomics combined with stable isotope labeling with amino acids in cell culture to identify proteins rapidly phosphorylated in response to GH in 3T3-F442A preadipocytes. We identified 132 phosphosites in 95 proteins that exhibited rapid (5 or 15 min) GH-dependent statistically significant increases in phosphorylation by more than or equal to 50% and 96 phosphosites in 46 proteins that were down-regulated by GH by more than or equal to 30%. Several of the GH-stimulated phosphorylation sites were known (e.g. regulatory Thr/Tyr in Erks 1 and 2, Tyr in signal transducers and activators of transcription (Stat) 5a and 5b, Ser939 in tuberous sclerosis protein (TSC) 2 or tuberin). The remaining 126 GH-stimulated sites were not previously associated with GH. Kyoto Encyclopedia of Genes and Genomes pathway analysis of GH-stimulated sites indicated enrichment in proteins associated with the insulin and mammalian target of rapamycin (mTOR) pathways, regulation of the actin cytoskeleton, and focal adhesions. Akt/protein kinase A consensus sites (RXRXXS/T) were the most commonly phosphorylated consensus sites. Immunoblotting confirmed GH-stimulated phosphorylation of all seven novel GH-dependent sites tested [regulatory sites in proline-rich Akt substrate, 40 kDA (PRAS40), regulatory associated protein of mTOR, ATP-citrate lyase, Na+/H+ exchanger-1, N-myc downstream regulated gene 1, and Shc]). The immunoblot results suggest that many, if not most, of the GH-stimulated phosphosites identified in this large-scale quantitative phosphoproteomics analysis, including sites in multiple proteins in the Akt/ mTOR complex 1 pathway, are phosphorylated in response to GH. Their identification significantly broadens our thinking of GH-regulated cell functions.
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Affiliation(s)
- Bridgette N Ray
- Departments of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Lin H, Ou J, Zhang Z, Dong J, Wu M, Zou H. Facile Preparation of Zwitterionic Organic-Silica Hybrid Monolithic Capillary Column with an Improved “One-Pot” Approach for Hydrophilic-Interaction Liquid Chromatography (HILIC). Anal Chem 2012; 84:2721-8. [DOI: 10.1021/ac3001429] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Hui Lin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Zhenbin Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Minghuo Wu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- College of Environmental and Chemical
Engineering, Nanchang Hangkong University, Nanchang 330063, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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34
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Affiliation(s)
- Carol L Nilsson
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, Texas 77555-0617, United States.
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35
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Wang F, Song C, Cheng K, Jiang X, Ye M, Zou H. Perspectives of Comprehensive Phosphoproteome Analysis Using Shotgun Strategy. Anal Chem 2011; 83:8078-85. [DOI: 10.1021/ac201833j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunxia Song
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xinning Jiang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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36
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Song C, Wang F, Ye M, Cheng K, Chen R, Zhu J, Tan Y, Wang H, Figeys D, Zou H. Improvement of the quantification accuracy and throughput for phosphoproteome analysis by a pseudo triplex stable isotope dimethyl labeling approach. Anal Chem 2011; 83:7755-62. [PMID: 21902226 DOI: 10.1021/ac201299j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Accurately quantifying the changes of phosphorylation level on specific sites is crucial to understand the role of protein phosphorylation in physiological and pathological processes. Here, a pseudo triplex stable isotope dimethyl labeling approach was developed to improve the accuracy and the throughput of comprehensive quantitative phosphoproteome analyses. In this strategy, two identical samples are labeled with light and heavy isotopes, respectively, while another comparative sample is labeled with an intermediate isotope. Two replicated quantification results were achieved in just one experiment, and the relative standard deviation (RSD) criterion was used to control the quantification accuracy. Compared with the conventional duplex labeling approach, the number of quantified phosphopeptides increased nearly 50% and the experimental time was reduced by 50% under the same quantification accuracy. Combined with the automated online reversed phase-strong cation exchange-reversed phase (RP-SCX-RP) multidimensional separation system, a comparative phosphoproteome analysis of hepatocellular carcinoma (HCC) and normal human liver tissues was performed. Over 1800 phosphopeptides corresponding to ~2000 phosphorylation sites were quantified reliably in a 42 h multidimensional analysis. The pro-directed motifs, which were mainly associated with the extracellular signal-regulated kinases (ERKs), were observed as being overrepresented in the regulated phosphorylation sites, and some quantification results of phosphorylation sites were validated by the other studies. Therefore, this pseudo triplex labeling approach was demonstrated as a promising alternative for the comprehensive quantitative phosphoproteome analysis.
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Affiliation(s)
- Chunxia Song
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Leitner A, Sturm M, Lindner W. Tools for analyzing the phosphoproteome and other phosphorylated biomolecules: a review. Anal Chim Acta 2011; 703:19-30. [PMID: 21843671 DOI: 10.1016/j.aca.2011.07.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/07/2011] [Accepted: 07/10/2011] [Indexed: 11/28/2022]
Abstract
Enrichment, separation and mass spectrometric analysis of biomolecules carrying a phosphate group plays an important role in current analytical chemistry. Application areas range from the preparative enrichment of phospholipids for biotechnological purposes and the separation and purification of plasmid DNA or mRNA to the specific preconcentration of phosphoproteins and -peptides to facilitate their later identification and characterization by mass spectrometry. Most of the recent improvements in this field were triggered by the need for phosphopeptide enrichment technology for the analysis of cellular protein phosphorylation events with the help of liquid chromatography-mass spectrometry. The high sensitivity of mass spectrometry and the possibility to combine this technique with different separation modes in liquid chromatography have made it the method of choice for proteome analysis. However, in the case of phosphoprotein analysis, the low abundance of the resulting phosphopeptides and their low quality fragment spectra interfere with the identification of phosphorylation events. Recent developments in phosphopeptide enrichment and fragmentation technologies successfully helped to overcome these limitations. In this review, we will focus on sample preparation techniques in the field of phosphoproteomics, but also highlight recent advancements for the analysis of other phosphorylated biomolecules.
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