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Lin JD, Stogios PJ, Abe KT, Wang A, MacPherson J, Skarina T, Gingras AC, Savchenko A, Ensminger AW. Functional diversification despite structural congruence in the HipBST toxin-antitoxin system of Legionella pneumophila. mBio 2023; 14:e0151023. [PMID: 37819088 PMCID: PMC10653801 DOI: 10.1128/mbio.01510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Toxin-antitoxin (TA) systems are parasitic genetic elements found in almost all bacterial genomes. They are exchanged horizontally between cells and are typically poorly conserved across closely related strains and species. Here, we report the characterization of a tripartite TA system in the bacterial pathogen Legionella pneumophila that is highly conserved across Legionella species genomes. This system (denoted HipBSTLp) is a distant homolog of the recently discovered split-HipA system in Escherichia coli (HipBSTEc). We present bioinformatic, molecular, and structural analyses of the divergence between these two systems and the functionality of this newly described TA system family. Furthermore, we provide evidence to refute previous claims that the toxin in this system (HipTLp) possesses bifunctionality as an L. pneumophila virulence protein. Overall, this work expands our understanding of the split-HipA system architecture and illustrates the potential for undiscovered biology in these abundant genetic elements.
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Affiliation(s)
- Jordan D. Lin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kento T. Abe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Avril Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John MacPherson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, Alberta, Canada
| | - Alexander W. Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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2
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Peng J, Chan C, Zhang S, Sklavounos AA, Olson ME, Scott EY, Hu Y, Rajesh V, Li BB, Chamberlain MD, Zhang S, Peng H, Wheeler AR. All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis. Chem Sci 2023; 14:2887-2900. [PMID: 36937585 PMCID: PMC10016607 DOI: 10.1039/d3sc00560g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Highly sensitive and reproducible analysis of samples containing low amounts of protein is restricted by sample loss and the introduction of contaminants during processing. Here, we report an All-in-One digital microfluidic (DMF) pipeline for proteomic sample reduction, alkylation, digestion, isotopic labeling and analysis. The system features end-to-end automation, with integrated thermal control for digestion, optimized droplet additives for sample manipulation and analysis, and an automated interface to liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Dimethyl labeling was integrated into the pipeline to allow for relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples. Several known proteins (including HSP90AB1, HSPB1, LDHA, ENO1, PGK1, KRT18, and AKR1C2) and pathways were observed between model breast cancer cell lines related to hormone response, cell metabolism, and cell morphology. Furthermore, differentially quantified proteins (such as PGS2, UGDH, ASPN, LUM, COEA1, and PRELP) were found in comparisons of healthy and cancer breast tissues, suggesting potential utility of the All-in-One pipeline for the emerging application of proteomic cancer sub-typing. In sum, the All-in-One pipeline represents a powerful new tool for automated proteome processing and analysis, with the potential to be useful for evaluating mass-limited samples for a wide range of applications.
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Affiliation(s)
- Jiaxi Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Calvin Chan
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Shuailong Zhang
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Mechatronical Engineering, Beijing Institute of Technology Beijing 100081 China
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, Beijing Institute of Technology Beijing 100081 China
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
| | - Maxwell E Olson
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Erica Y Scott
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Yechen Hu
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Vigneshwar Rajesh
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Bingyu B Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
- Saskatchewan Cancer Agency, University of Saskatchewan 107 Wiggins Road Saskatoon SK S7N 5E5 Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue Toronto ON M5G 1X5 Canada
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha Hunan 410000 China
| | - Hui Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Environment, University of Toronto 33 Willcocks Street Toronto ON M5S 3E8 Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
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3
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Han X, Zhang Y, Qiao O, Ji H, Zhang X, Wang W, Li X, Wang J, Li D, Ju A, Liu C, Gao W. Proteomic Analysis Reveals the Protective Effects of Yiqi Fumai Lyophilized Injection on Chronic Heart Failure by Improving Myocardial Energy Metabolism. Front Pharmacol 2021; 12:719532. [PMID: 34630097 PMCID: PMC8494180 DOI: 10.3389/fphar.2021.719532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/03/2021] [Indexed: 12/28/2022] Open
Abstract
Yiqi Fumai lyophilized injection (YQFM) is the recombination of Sheng mai san (SMS).YQFM has been applied clinically to efficaciously and safely treat chronic heart failure (CHF). However, the mechanism of YQFM is still not fully elucidated. The purpose of our study was to investigate the protective mechanism of YQFM against abdominal aortic coarctation (AAC) in rats by proteomic methods. After YQFM treatment, the cardiac function were obviously meliorated. One hundred and fifty-seven important differentially expressed proteins (DEPs) were identified, including 109 in model rat compared with that in control rat (M:C) and 48 in YQFM-treated rat compared with that in model rat (T:M) by iTRAQ technology to analyze the proteomic characteristics of heart tissue. Bioinformatics analysis showed that DEPs was mainly involved in the body’s energy metabolism and was closely related to oxidative phosphorylation. YQFM had also displayed efficient mitochondrial dysfunction alleviation properties in hydrogen peroxide (H2O2)-induced cardiomyocyte damage by Transmission Electron Microscope (TEM), Metabolic assay, and Mitotracker staining. What’s more, the levels of total cardiomyocyte apoptosis were markedly reduced following YQFM treatment. Furthermore, Western blot analysis showed that the expressions of peroxisome proliferator activated receptor co-activator-1α(PGC-1α) (p < 0.01 or p < 0.001), perixisome proliferation-activated receptor alpha (PPAR-α) (p < 0.001)and retinoid X receptor alpha (RXR-α) were upregulated (p < 0.001), PGC-1α as well as its downstream effectors were also found to be upregulated in cardiomyocytes after YQFM treatment(p < 0.001).These results provided evidence that YQFM could enhance mitochondrial function of cardiomyocytes to play a role in the treatment of CHF by regulating mitochondrial biogenesis-related proteins.
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Affiliation(s)
- Xiaoying Han
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yi Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Ou Qiao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Haixia Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xinyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Wenzhe Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xia Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Dekun Li
- Tasly Pride Pharmaceutical Company Limited, Tianjin, China
| | - Aichun Ju
- Tasly Pride Pharmaceutical Company Limited, Tianjin, China
| | - Changxiao Liu
- Tianjin Pharmaceutical Research Institute, Tianjin, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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5
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Perez SM, Brinton LT, Kelly KA. Plectin in Cancer: From Biomarker to Therapeutic Target. Cells 2021; 10:2246. [PMID: 34571895 PMCID: PMC8469460 DOI: 10.3390/cells10092246] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/17/2022] Open
Abstract
The cytolinker and scaffolding protein, plectin, has emerged as a potent driver of malignant hallmarks in many human cancers due to its involvement in various cellular activities contributing to tumorigenesis, including cancer cell proliferation, adhesion, migration, invasion, and signal transduction. Evidence shows that beyond plectin's diverse protein interactome, its cancer-specific mislocalization to the cell surface enables its function as a potent oncoprotein. As such, therapeutic targeting of plectin, its protein interactors, and, in particular, cancer-specific plectin (CSP) presents an attractive opportunity to impede carcinogenesis directly. Here, we report on plectin's differential gene and protein expression in cancer, explore its mutational profile, and discuss the current understanding of plectin's and CSP's biological function in cancer. Moreover, we review the landscape of plectin as a prognostic marker, diagnostic biomarker, and target for imaging and therapeutic modalities. We highlight how, beyond their respective biological importance, plectin's common overexpression in cancer and CSP's cancer-specific bioavailability underscore their potential as high-value druggable targets. We discuss how recent evidence of the potent anti-cancer effects of CSP therapeutic targeting opens the door for cell-surface mislocalized proteins as novel therapeutic targets.
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Affiliation(s)
- Samantha M. Perez
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA;
| | | | - Kimberly A. Kelly
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA;
- ZielBio, Inc., Charlottesville, VA 22903, USA
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6
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Abyadeh M, Meyfour A, Gupta V, Zabet Moghaddam M, Fitzhenry MJ, Shahbazian S, Hosseini Salekdeh G, Mirzaei M. Recent Advances of Functional Proteomics in Gastrointestinal Cancers- a Path towards the Identification of Candidate Diagnostic, Prognostic, and Therapeutic Molecular Biomarkers. Int J Mol Sci 2020; 21:ijms21228532. [PMID: 33198323 PMCID: PMC7697099 DOI: 10.3390/ijms21228532] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/02/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) cancer remains one of the common causes of morbidity and mortality. A high number of cases are diagnosed at an advanced stage, leading to a poor survival rate. This is primarily attributed to the lack of reliable diagnostic biomarkers and limited treatment options. Therefore, more sensitive, specific biomarkers and curative treatments are desirable. Functional proteomics as a research area in the proteomic field aims to elucidate the biological function of unknown proteins and unravel the cellular mechanisms at the molecular level. Phosphoproteomic and glycoproteomic studies have emerged as two efficient functional proteomics approaches used to identify diagnostic biomarkers, therapeutic targets, the molecular basis of disease and mechanisms underlying drug resistance in GI cancers. In this review, we present an overview on how functional proteomics may contribute to the understanding of GI cancers, namely colorectal, gastric, hepatocellular carcinoma and pancreatic cancers. Moreover, we have summarized recent methodological developments in phosphoproteomics and glycoproteomics for GI cancer studies.
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Affiliation(s)
- Morteza Abyadeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; (M.A.); (G.H.S.)
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 1985717413, Iran
- Cell Science Research Center, Department of Stem Cells and Developmental Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
- Correspondence: (A.M.); (M.M.)
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | | | - Matthew J. Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | - Shila Shahbazian
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | - Ghasem Hosseini Salekdeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; (M.A.); (G.H.S.)
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2113, Australia;
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW 2113, Australia;
- Correspondence: (A.M.); (M.M.)
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7
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Xu C, Zhang J, Liu J, Li Z, Liu Z, Luo Y, Xu Q, Wang M, Zhang G, Wang F, Chen H. Proteomic analysis reveals the protective effects of emodin on severe acute pancreatitis induced lung injury by inhibiting neutrophil proteases activity. J Proteomics 2020; 220:103760. [PMID: 32244009 DOI: 10.1016/j.jprot.2020.103760] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/04/2020] [Accepted: 03/23/2020] [Indexed: 02/08/2023]
Abstract
Acute lung injury (ALI) is the most common remote organ complication induced by severe acute pancreatitis (SAP). Almost 60-70% SAP-induced deaths are caused by ALI. Efficient clinical therapeutic strategy for SAP-induced ALI is still lacking. In this study, we demonstrate that Emodin (EMO) can significantly alleviate SAP-induced ALI. We investigate the therapeutic mechanisms of EMO by proteomic analysis, which indicates that EMO protects lung tissue against SAP-ALI by negative regulation of endopeptidase activity and inhibition of collagen-containing extracellular matrix degradation. Protein-protein interaction analysis showed Lamc2, Serpina1 and Serpinb1 play important roles in the above pathways. This study elucidates the possible mechanism and suggests the candidacy of EMO in the clinical treatment of SAP-ALI. SIGNIFICANCE: ALI is a major leading cause of death in SAP. DEX is the standard of care drug for treatment of SAP-ALI, but often associated with inevitable side effects. In the present study, EMO was demonstrated to greatly alleviate the lung injury induced by SAP. Through proteomic analysis, the recovered protein profiles in response to EMO treatment in SAP-ALI rat models was obtained, among which Lamc2, Serpina1 and Serpinb1 were discovered as crucial regulatory proteins in SAP-ALI disease. Our study provides the underlying mechanisms and novel targets of EMO protective effect against SAP-ALI.
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Affiliation(s)
- Caiming Xu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China; Department of Traditional Chinese Medicine, Dalian Obstetrics and Gynecology Hospital, Dalian 116021, China
| | - Jingyu Zhang
- CAS key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning Province 116023, China
| | - Jing Liu
- Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China; CAS key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning Province 116023, China
| | - Zhaoxia Li
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Zheyi Liu
- CAS key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning Province 116023, China
| | - Yalan Luo
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Qiushi Xu
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Mengfei Wang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Guixin Zhang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China
| | - 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 (CAS), Dalian, Liaoning Province 116023, China.
| | - Hailong Chen
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; Institute (College) of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, Liaoning 116044, China.
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8
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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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9
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Sun B, Liu Z, Fang Z, Dong W, Yu Y, Ye M, Liu L, Wang H, Wang F. Probing the Proteomics Dark Regions by VAILase Cleavage at Aliphatic Amino Acids. Anal Chem 2020; 92:2770-2777. [PMID: 31903742 DOI: 10.1021/acs.analchem.9b05048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteomics emerges from the protein identification to protein functional elucidation, which depends to a large extent on the characterization of protein sequences. However, a large part of proteome sequences remains unannotated due to the limitation in proteolytic digestion by golden standard protease trypsin. Herein, we demonstrated that a cyanobacterial protease VAILase could specifically cleave at the short-chain aliphatic amino acids valine, alanine, leucine, isoleucine and threonine with cleavage specificity about 92% in total for proteomic analysis. The unique features of VAILase cleavage facilitate the characterization of most proteins and exhibit high complementarity to trypsin, and 22% of the covered sequences by VAILase are unique. VAILase can greatly improve the coverages of sequences with abundant aliphatic residues that are usually dark regions in conventional proteomic analysis, such as the transmembrane regions within anion exchanger 1 and photosystem II.
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Affiliation(s)
- Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China
| | - Zheng Fang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Wei Dong
- CAS Key Laboratory of Photobiology , Institute of Botany, Chinese Academy of Sciences , Beijing , 100049 , China
| | - Yang Yu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , 130022 , China.,University of Science and Technology of China , Hefei , 230026 , China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China
| | - Lin Liu
- CAS Key Laboratory of Photobiology , Institute of Botany, Chinese Academy of Sciences , Beijing , 100049 , China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , 130022 , China.,University of Science and Technology of China , Hefei , 230026 , China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
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11
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Liu Z, Wang R, Liu J, Sun R, Wang F. Global Quantification of Intact Proteins via Chemical Isotope Labeling and Mass Spectrometry. J Proteome Res 2019; 18:2185-2194. [PMID: 30990045 DOI: 10.1021/acs.jproteome.9b00071] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although thousands of intact proteins have been feasibly identified in recent years, global quantification of intact proteins is still challenging. Herein, we develop a high-throughput strategy for global intact protein quantification based on chemical isotope labeling. The isotope incorporation efficiency is as high as 99.2% for complex intact protein samples extracted from HeLa cells. Further, the pTop 2.0 software is developed for automated quantification of intact proteoforms in a high-throughput manner. The high quantification accuracy and reproducibility of this strategy have been demonstrated for both standard and complex cellular protein samples. A total of 2283 intact proteoforms originated from 660 protein accessions are successfully quantified under anaerobic and aerobic conditions and the differentially expressed proteins are observed to be involved in the important biological processes such as stress response.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , 116023 , China
| | - Ruimin Wang
- Institute of Computing Technology , Chinese Academy of Sciences , Beijing , 100190 , China
| | - Jing Liu
- College of Pharmacy , Dalian Medical University , Dalian , 116044 , China
| | - Ruixiang Sun
- Institute of Computing Technology , Chinese Academy of Sciences , Beijing , 100190 , China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian , 116023 , China
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12
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Yao M, Liu Y, Fei L, Zhou Y, Wang F, Chen J. Self-Adaptable Quinone-Quinol Exchange Mechanism of Photosystem II. J Phys Chem B 2018; 122:10478-10489. [PMID: 30380868 DOI: 10.1021/acs.jpcb.8b09641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The step of plastoquinone (PQ) reduction to plastoquinol (PQH2) can regulate the photoreaction rate of photosystem II (PSII). To experimentally unravel the PQ-PQH2 exchange mechanism of PSII, we investigate the reaction kinetics of plant PSII membranes and the subunits-trimmed PSII core complexes with various PQ analogues and directly probe the reductions of PQ and other quinones by 257 nm resonance Raman scattering. Two phases of quinone concentration effect on the reaction rate originate from the quinone-quinol exchange mechanism. The results indicate that high concentrations of quinone, more than one movable quinone molecule per PSII reaction center, could trigger quinone-quinol exchange adapting to the unidirectional route: quinones enter through channel I and/or III, and quinols leave through channel II. A weak quinone binding site near QB probably plays a crucial role in pushing quinone-quinol exchange forward in the unidirectional route. Our work provides experimental proofs demonstrating a self-adaptable quinone-quinol exchange mechanism of PSII.
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Affiliation(s)
- Mingdong Yao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China.,Key Laboratory of Systems Bioengineering (Ministry of Education) , Tianjin University , Tianjin 300072 , China
| | - Ying Liu
- Institute of Materials , China Academy of Engineering Physics , Mianyang 621907 , China
| | - Liping Fei
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China
| | - Ye Zhou
- 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
| | - Fangjun Wang
- 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
| | - Jun Chen
- Science and Technology on Surface Physics and Chemistry Laboratory , Jiangyou 621908 , China.,State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China
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13
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14
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Yu Q, Shi X, Feng Y, Kent KC, Li L. Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies. Anal Chim Acta 2017; 968:40-49. [PMID: 28395773 PMCID: PMC5509462 DOI: 10.1016/j.aca.2017.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/03/2017] [Accepted: 03/02/2017] [Indexed: 11/22/2022]
Abstract
Mass spectrometry (MS)-based isobaric labeling has undergone rapid development in recent years due to its capability for high throughput quantitation. Apart from its originally designed use with collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), isobaric tagging technique could also work with electron-transfer dissociation (ETD), which provides complementarity to CID and is preferred in sequencing peptides with post-translational modifications (PTMs). However, ETD suffers from long reaction time, reduced duty cycle and bias against peptides with lower charge states. In addition, common fragmentation mechanism in ETD results in altered reporter ion production, decreased multiplexing capability, and even loss of quantitation capability for some of the isobaric tags, including custom-designed dimethyl leucine (DiLeu) tags. Here, we demonstrate a novel electron-transfer/higher-energy collision dissociation (EThcD) approach that preserves original reporter ion channels, mitigates bias against lower charge states, improves sensitivity, and significantly improves data quality for quantitative proteomics and proteome-wide PTM studies. Systematic optimization was performed to achieve a balance between data quality and sensitivity. We provide direct comparison of EThcD with ETD and HCD for DiLeu- and TMT-labeled HEK cell lysate and IMAC enriched phosphopeptides. Results demonstrate improved data quality and phosphorylation localization accuracy while preserving sufficient reporter ion production. Biological studies were performed to investigate phosphorylation changes in a mouse vascular smooth muscle cell line treated with four different conditions. Overall, EThcD exhibits superior performance compared to conventional ETD and offers distinct advantages compared to HCD in isobaric labeling based quantitative proteomics and quantitative PTM studies.
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Affiliation(s)
- Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Xudong Shi
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Yu Feng
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - K Craig Kent
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA.
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15
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Lin YT, Chien KY, Wu CC, Chang WY, Chu LJ, Chen MC, Yeh CT, Yu JS. Super-SILAC mix coupled with SIM/AIMS assays for targeted verification of phosphopeptides discovered in a large-scale phosphoproteome analysis of hepatocellular carcinoma. J Proteomics 2017; 157:40-51. [DOI: 10.1016/j.jprot.2017.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/23/2017] [Accepted: 02/08/2017] [Indexed: 01/04/2023]
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16
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Liu J, Xu B, Liu Z, Dong M, Mao J, Zhou Y, Chen J, Wang F, Zou H. Specific mixing facilitates the comparative quantification of phosphorylation sites with significant dysregulations. Anal Chim Acta 2017; 950:129-137. [DOI: 10.1016/j.aca.2016.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 11/27/2022]
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17
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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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Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient. Proc Natl Acad Sci U S A 2016; 113:1381-6. [PMID: 26787912 DOI: 10.1073/pnas.1523434113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Compensatory signaling pathways in tumors confer resistance to targeted therapy, but the pathways and their mechanisms of activation remain largely unknown. We describe a procedure for quantitative proteomics and phosphoproteomics on snap-frozen biopsies of hepatocellular carcinoma (HCC) and matched nontumor liver tissue. We applied this procedure to monitor signaling pathways in serial biopsies taken from an HCC patient before and during treatment with the multikinase inhibitor sorafenib. At diagnosis, the patient had an advanced HCC. At the time of the second biopsy, abdominal imaging revealed progressive disease despite sorafenib treatment. Sorafenib was confirmed to inhibit MAPK signaling in the tumor, as measured by reduced ribosomal protein S6 kinase phosphorylation. Hierarchical clustering and enrichment analysis revealed pathways broadly implicated in tumor progression and resistance, such as epithelial-to-mesenchymal transition and cell adhesion pathways. Thus, we describe a protocol for quantitative analysis of oncogenic pathways in HCC biopsies and obtained first insights into the effect of sorafenib in vivo. This protocol will allow elucidation of mechanisms of resistance and enable precision medicine.
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Zhang S, Yuan H, Zhao B, Zhou Y, Jiang H, Zhang L, Liang Z, Zhang Y. Integrated platform with a combination of online digestion and (18)O labeling for proteome quantification via an immobilized trypsin microreactor. Analyst 2016; 140:5227-34. [PMID: 26063120 DOI: 10.1039/c5an00887e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A novel automated integrated platform for quantitative proteome analysis was established with a combination of online digestion of proteins and in situ(18)O labeling by an immobilized enzyme reactor (IMER); digests were captured and desalted by a C18 trap column, and peptides were analyzed by nanoRPLC-ESI-MS/MS. Bovine serum albumin (BSA) was used to evaluate the performance of the developed platform. Compared with traditional offline methods, not only the digestion and labeling time was shortened from 36 h to just 1 h, but also the labeling efficiency was improved from 95% to 99%. Furthermore, the back-exchange from (18)O to (16)O could also be efficiently avoided by the use of IMER. The platform was further evaluated by the quantitative analysis of 100 ng (18)O and (16)O online labeled yeast sample with a mixing ratio of 1 : 1, and the results showed significantly improved sensitivity and reproducibility, as well as improved quantitative accuracy than offline method. With these advantages, the integrated platform was finally applied to the quantitative profiling of 100 ng proteins extracted from two mouse hepatocarcinoma ascites syngeneic cell lines with high and low lymph node metastases rates, and ten differentially expressed proteins were successfully found, most of which were related to tumorigenesis and tumor metastasis. All these results demonstrate that the developed integrated platform can provide a new way for high efficiency (18)O labeling and the quantitative analysis of trace amounts of sample with high accuracy and high reproducibility.
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Affiliation(s)
- Shen Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China.
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20
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Huang G, Sun Z, Qin H, Zhao L, Xiong Z, Peng X, Ou J, Zou H. Preparation of hydrazine functionalized polymer brushes hybrid magnetic nanoparticles for highly specific enrichment of glycopeptides. Analyst 2015; 139:2199-206. [PMID: 24615010 DOI: 10.1039/c4an00076e] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydrazide chemistry is a powerful technique in glycopeptides enrichment. However, the low density of the monolayer hydrazine groups on the conventional hydrazine-functionalized magnetic nanoparticles limits the efficiency of glycopeptides enrichment. Herein, a novel magnetic nanoparticle grafted with poly(glycidyl methacrylate) (GMA) brushes was fabricated via reversible addition-fragmentation chain transfer (RAFT) polymerization, and a large amount of hydrazine groups were further introduced to the GMA brushes by ring-opening the epoxy groups with hydrazine hydrate. The resulting magnetic nanoparticles (denoted as Fe3O4@SiO2@GMA-NHNH2) demonstrated the high specificity of capturing glycopeptides from a tryptic digest of the sample comprising a standard non-glycosylated protein bovine serum albumin (BSA) and four standard glycoproteins with a weight ratio of 50 : 1, and the detection limit was as low as 130 fmol. In the analysis of a real complex biological sample, the tryptic digest of hepatocellular carcinoma, 179 glycosites were identified by the Fe3O4@SiO2@GMA-NHNH2 nanoparticles, surpassing that of 68 glycosites by Fe3O4@SiO2-single-NHNH2 (with monolayer hydrazine groups on the surface). It can be expected that the magnetic nanoparticles modified with hydrazine functionalized polymer brushes via RAFT technique will improve the specificity and the binding capacity of glycopeptides from complex samples, and show great potential in the analysis of protein glycosylation in biological samples.
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Affiliation(s)
- Guang Huang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.
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21
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Huang J, Qin H, Sun Z, Huang G, Mao J, Cheng K, Zhang Z, Wan H, Yao Y, Dong J, Zhu J, Wang F, Ye M, Zou H. A peptide N-terminal protection strategy for comprehensive glycoproteome analysis using hydrazide chemistry based method. Sci Rep 2015; 5:10164. [PMID: 25959593 PMCID: PMC4426672 DOI: 10.1038/srep10164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/01/2015] [Indexed: 01/01/2023] Open
Abstract
Enrichment of glycopeptides by hydrazide chemistry (HC) is a popular method for glycoproteomics analysis. However, possible side reactions of peptide backbones during the glycan oxidation in this method have not been comprehensively studied. Here, we developed a proteomics approach to locate such side reactions and found several types of the side reactions that could seriously compromise the performance of glycoproteomics analysis. Particularly, the HC method failed to identify N-terminal Ser/Thr glycopeptides because the oxidation of vicinal amino alcohol on these peptides generates aldehyde groups and after they are covalently coupled to HC beads, these peptides cannot be released by PNGase F for identification. To overcome this drawback, we apply a peptide N-terminal protection strategy in which primary amine groups on peptides are chemically blocked via dimethyl labeling, thus the vicinal amino alcohols on peptide N-termini are eliminated. Our results showed that this strategy successfully prevented the oxidation of peptide N-termini and significantly improved the coverage of glycoproteome.
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Affiliation(s)
- Junfeng Huang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang Huang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Wan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jun Zhu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - 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, 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, 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, China
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Shalit T, Elinger D, Savidor A, Gabashvili A, Levin Y. MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer. J Proteome Res 2015; 14:1979-86. [PMID: 25780947 DOI: 10.1021/pr501045t] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Presented is a data set for benchmarking MS1-based label-free quantitative proteomics using a quadrupole orbitrap mass spectrometer. Escherichia coli digest was spiked into a HeLa digest in four different concentrations, simulating protein expression differences in a background of an unchanged complex proteome. The data set provides a unique opportunity to evaluate the proteomic platform (instrumentation and software) in its ability to perform MS1-intensity-based label-free quantification. We show that the presented combination of informatics and instrumentation produces high precision and quantification accuracy. The data were also used to compare different quantitative protein inference methods such as iBAQ and Hi-N. The data can also be used as a resource for development and optimization of proteomics informatics tools, thus the raw data have been deposited to ProteomeXchange with identifier PXD001385.
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Affiliation(s)
- Tali Shalit
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dalia Elinger
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alon Savidor
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alexandra Gabashvili
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yishai Levin
- †de Botton Institute for Protein Profiling and ‡Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
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Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor. Proc Natl Acad Sci U S A 2015; 112:E1594-603. [PMID: 25829543 DOI: 10.1073/pnas.1503286112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Systematic characterization of intercellular signaling approximating the physiological conditions of stimulation that involve direct cell-cell contact is challenging. We describe a proteomic strategy to analyze physiological signaling mediated by the T-cell costimulatory receptor CD28. We identified signaling pathways activated by CD28 during direct cell-cell contact by global analysis of protein phosphorylation. To define immediate CD28 targets, we used phosphorylated forms of the CD28 cytoplasmic region to obtain the CD28 interactome. The interaction profiles of selected CD28-interacting proteins were further characterized in vivo for amplifying the CD28 interactome. The combination of the global phosphorylation and interactome analyses revealed broad regulation of CD28 and its interactome by phosphorylation. Among the cellular phosphoproteins influenced by CD28 signaling, CapZ-interacting protein (CapZIP), a regulator of the actin cytoskeleton, was implicated by functional studies. The combinatorial approach applied herein is widely applicable for characterizing signaling networks associated with membrane receptors with short cytoplasmic tails.
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Puangpila C, Mayadunne E, El Rassi Z. Liquid phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2011-2014. Electrophoresis 2015; 36:238-52. [PMID: 25287967 PMCID: PMC4485988 DOI: 10.1002/elps.201400434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 11/07/2022]
Abstract
This review article expands on the previous one (S. Selvaraju and Z. El Rassi, Electrophoresis 2012, 33, 74-88) by reviewing pertinent literature in the period extending from early 2011 to present. As the previous review article, the present one is concerned with proteomic sample preparation (e.g., depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article, however, is distinguished from its earlier version by expanding on capturing/enriching subphosphoproteomes by immobilized metal affinity chromatography and metal oxide affinity chromatography. Seventy-seven papers published in the period extending from mid-2011 to the present have been reviewed. By no means this review article is exhaustive, given the fact that its aim is to give a concise treatment of the latest developments in the field.
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Affiliation(s)
- Chanida Puangpila
- Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
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25
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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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Recent advances in stable isotope labeling based techniques for proteome relative quantification. J Chromatogr A 2014; 1365:1-11. [PMID: 25246102 DOI: 10.1016/j.chroma.2014.08.098] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/24/2014] [Accepted: 08/27/2014] [Indexed: 12/27/2022]
Abstract
The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected.
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27
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Wu Y, Wang F, Liu Z, Qin H, Song C, Huang J, Bian Y, Wei X, Dong J, Zou H. Five-plex isotope dimethyl labeling for quantitative proteomics. Chem Commun (Camb) 2014; 50:1708-10. [PMID: 24394284 DOI: 10.1039/c3cc47998f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stable isotope dimethyl labeling, a widely used method for quantitative proteomics, was extended to five channels for the first time. Comprehensive proteome and phosphoproteome quantification validated the high quantification accuracy and throughput of this five-plex method.
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Affiliation(s)
- Yue Wu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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28
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Zhao B, Xu B, Hu W, Song C, Wang F, Liu Z, Ye M, Zou H, Miao QR. Comprehensive proteome quantification reveals NgBR as a new regulator for epithelial-mesenchymal transition of breast tumor cells. J Proteomics 2014; 112:38-52. [PMID: 25173099 DOI: 10.1016/j.jprot.2014.08.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/22/2014] [Accepted: 08/04/2014] [Indexed: 12/13/2022]
Abstract
UNLABELLED Nogo-B receptor (NgBR) is a type I receptor and specifically binds to ligand Nogo-B. Our previous work has shown that NgBR is highly expressed in human breast invasive ductal carcinoma. Here, comprehensive proteome quantification was performed to examine the alteration of protein expression profile in MDA-MB-231 breast tumor cells after knocking down NgBR using lentivirus-mediated shRNA approach. Among a total of 1771 proteins feasibly quantified, 994 proteins were quantified in two biological replicates with RSD <50%. There are 122 proteins significantly down-regulated in NgBR knockdown MDA-MB-231 breast tumor cells, such as vimentin and S100A4, well-known markers for mesenchymal cells, and CD44, a stemness indicator. The decrease of vimentin, S100A4 and CD44 protein expression levels was further confirmed by Western blot analysis. MDA-MB-231 cells are typical breast invasive ductal carcinoma cells showing mesenchymal phenotype. Cell morphology analysis demonstrates NgBR knockdown in MDA-MB-231 cells results in reversibility of epithelial-mesenchymal transition (EMT), which is one of the major mechanisms involved in breast cancer metastasis. Furthermore, we demonstrated that NgBR knockdown in MCF-7 cells significantly prevented the TGF-β-induced EMT process as determined by the morphology change, and staining of E-cadherin intercellular junction as well as the decreased expression of vimentin. BIOLOGICAL SIGNIFICANCE Our previous publication showed that NgBR is highly expressed in human breast invasive ductal carcinoma. However, the roles of NgBR and NgBR-mediated signaling pathway in breast tumor cells are still unclear. Here, we not only demonstrated that the quantitative proteomics analysis is a powerful tool to investigate the global biological function of NgBR, but also revealed that NgBR is involved in the transition of breast epithelial cells to mesenchymal stem cells, which is one of the major mechanisms involved in breast cancer metastasis. These findings provide new insights for understanding the roles of NgBR in regulating breast epithelial cell transform during the pathogenesis of breast cancer.
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Affiliation(s)
- Baofeng Zhao
- Division of Pediatric Surgery, Department of Surgery, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Pediatric Pathology, Department of Pathology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Bo Xu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wenquan Hu
- Division of Pediatric Surgery, Department of Surgery, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Pediatric Pathology, Department of Pathology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chunxia Song
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Fangjun Wang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhong Liu
- Division of Pediatric Surgery, Department of Surgery, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Pediatric Pathology, Department of Pathology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hanfa Zou
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Qing R Miao
- Division of Pediatric Surgery, Department of Surgery, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Pediatric Pathology, Department of Pathology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion. Anal Bioanal Chem 2014; 406:6247-56. [DOI: 10.1007/s00216-014-8071-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/14/2014] [Accepted: 07/25/2014] [Indexed: 11/25/2022]
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Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development. SCIENCE CHINA-LIFE SCIENCES 2014; 57:1162-71. [PMID: 25119674 DOI: 10.1007/s11427-014-4714-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/01/2014] [Indexed: 12/17/2022]
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Huang J, Qin H, Dong J, Song C, Bian Y, Dong M, Cheng K, Wang F, Sun D, Wang L, Ye M, Zou H. In situ sample processing approach (iSPA) for comprehensive quantitative phosphoproteome analysis. J Proteome Res 2014; 13:3896-904. [PMID: 25072903 DOI: 10.1021/pr500454g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Current sample preparation protocols for quantitative phosphoproteome analysis are tedious and time-consuming. Here, a facile in situ sample processing approach (iSPA) is developed by using macroporous Ti(IV)-IMAC microspheres as the preparation "beds", where all sample preparation procedures including the enrichment of phosphoproteins, tryptic digestion of proteins, enrichment, and isotope labeling of phosphopeptides are performed in situ sequentially. As a result of the in situ processing design and the seamless procedures, extra steps for desalting and buffer exchanging, which are always required in conventional approaches, are avoided, and the sample loss and contamination could be greatly reduced. Thus, better sensitivity and accuracy for the quantitative phosphoproteome analysis were obtained. This strategy was further applied to differential phosphoproteome analysis of human liver tissues with or without hepatocellular carcinoma (HCC). In total, 8548 phosphorylation sites were confidently quantified from three replicate analyses of 0.5 mg of human liver protein extracts.
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Affiliation(s)
- Junfeng Huang
- CAS Key Lab 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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Xu B, Wang F, Song C, Sun Z, Cheng K, Tan Y, Wang H, Zou H. Large-scale proteome quantification of hepatocellular carcinoma tissues by a three-dimensional liquid chromatography strategy integrated with sample preparation. J Proteome Res 2014; 13:3645-54. [PMID: 24972180 DOI: 10.1021/pr500200s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma is one of the most fatal cancers worldwide. In this study, a reversed-phase-strong cation exchange-reversed-phase three-dimensional liquid chromatography strategy was established and coupled with mass spectrometry to investigate the differential proteome expression of HCC and normal liver tissues. In total, 2759 proteins were reliably quantified, of which, 648 proteins were dysregulated more than 3-fold in HCC liver tissues. Some important proteins that relate to HCC pathology were significantly dysregulated, such as NAT2 and AKR1B10. Furthermore, 2307 phosphorylation sites from 1264 phosphoproteins were obtained in our previous phosphoproteome quantification, and the nonphosphorylated counterparts of 445 phosphoproteins with 983 phosphorylation sites were reliably quantified in this work. It was observed that 337 (34%) phosphorylation sites exhibit significantly different expression trends from that of their corresponding nonphosphoproteins. Some novel phosphorylation sites with important biological functions in the progression of HCC were reliably quantified, such as the significant downregulation of pT185 for ERK2 and pY204 for ERK1.
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Affiliation(s)
- Bo Xu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
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Liu F, Ye M, Pan Y, Zhang Y, Bian Y, Sun Z, Zhu J, Cheng K, Zou H. Integration of cell lysis, protein extraction, and digestion into one step for ultrafast sample preparation for phosphoproteome analysis. Anal Chem 2014; 86:6786-91. [PMID: 24958348 DOI: 10.1021/ac5002146] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Conventional sample preparation protocols for phosphoproteome analysis require multiple time-consuming and labor-intensive steps, including cell lysis, protein extraction, protein digestion, and phosphopeptide enrichment. In this study, we found that the presence of a large amount of trypsin in the sample did not interfere with phosphopeptide enrichment and subsequent LC-MS/MS analysis. Taking advantage of fast digestion achieved with high trypsin-to-protein ratio, we developed a novel concurrent lysis-digestion method for phosphoproteome analysis. In this method, the harvested cells were first placed in a lysis buffer containing a huge amount of trypsin. After ultrasonication, the cells were lysed and the proteins were efficiently digested into peptides within one step. Thereafter, tryptic digest was subjected to phosphopeptide enrichment, in which unphosphorylated peptides, trypsin, and other components incompatible with LC-MS/MS analysis were removed. Compared with conventional methods, better phosphoproteome coverage was achieved in this new one-step method. Because protein solubilization and cell lysis were facilitated by fast protein digestion, the complete transformation of cell pellets into the peptide mixture could be finished within 25 min, while it would take at least 16 h for conventional methods. Hence, our method, which integrated cell lysis, protein extraction, and protein digestion into one step, is rapid and convenient. It is expected to have broad applications in phosphoproteomics analysis.
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Affiliation(s)
- Fangjie Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China
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Sun Z, Sun D, Wang F, Cheng K, Zhang Z, Xu B, Ye M, Wang L, Zou H. Differential analysis of N-glycoproteome between hepatocellular carcinoma and normal human liver tissues by combination of multiple protease digestion and solid phase based labeling. Clin Proteomics 2014; 11:26. [PMID: 25097464 PMCID: PMC4112855 DOI: 10.1186/1559-0275-11-26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 04/23/2014] [Indexed: 12/25/2022] Open
Abstract
Background Dysregulation of glycoproteins is closely related with many diseases. Quantitative proteomics methods are powerful tools for the detection of glycoprotein alterations. However, in almost all quantitative glycoproteomics studies, trypsin is used as the only protease to digest proteins. This conventional method is unable to quantify N-glycosites in very short or long tryptic peptides and so comprehensive glycoproteomics analysis cannot be achieved. Methods In this study, a comprehensive analysis of the difference of N-glycoproteome between hepatocellular carcinoma (HCC) and normal human liver tissues was performed by an integrated workflow combining the multiple protease digestion and solid phase based labeling. The quantified N-glycoproteins were analyzed by GoMiner to obtain a comparative view of cellular component, biological process and molecular function. Results/conclusions An integrated workflow was developed which enabled the processes of glycoprotein coupling, protease digestion and stable isotope labeling to be performed in one reaction vessel. This workflow was firstly evaluated by analyzing two aliquots of the same protein extract from normal human liver tissue. It was demonstrated that the multiple protease digestion improved the glycoproteome coverage and the quantification accuracy. This workflow was further applied to the differential analysis of N-glycoproteome of normal human liver tissue and that with hepatocellular carcinoma. A total of 2,329 N-glycosites on 1,052 N-glycoproteins were quantified. Among them, 858 N-glycosites were quantified from more than one digestion strategy with over 99% confidence and 1,104 N-glycosites were quantified from only one digestion strategy with over 95% confidence. By comparing the GoMiner results of the N-glycoproteins with and without significant changes, the percentage of membrane and secreted proteins and their featured biological processes were found to be significant different revealing that protein glycosylation may play the vital role in the development of HCC.
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Affiliation(s)
- Zhen Sun
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Deguang Sun
- The Second Affiliated Hospital of Dalian Medical University, Dalian 116027, China
| | - Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kai Cheng
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhang Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Bo Xu
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Liming Wang
- The Second Affiliated Hospital of Dalian Medical University, Dalian 116027, China
| | - Hanfa Zou
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Selective chemoprecipitation to enrich nitropeptides from complex proteomes for mass-spectrometric analysis. Nat Protoc 2014; 9:882-95. [PMID: 24651500 DOI: 10.1038/nprot.2014.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Post-translational protein nitration has attracted interest owing to its involvement in cellular signaling, effects on protein function and potential as biomarker of nitroxidative stress. We describe a procedure for enriching nitropeptides for mass spectrometry (MS)-based proteomics that is a simple and reliable alternative to immunoaffinity-based methods. The starting material for this procedure is a proteolytic digest. The peptides are reacted with formaldehyde and sodium cyanoborohydride to dimethylate all the N-terminal and side chain amino groups. Sodium dithionite is added subsequently to reduce the nitro groups to amines; in theory, the only amino groups present will have originally been nitro groups. The peptide sample is then applied to a solid-phase active ester reagent (SPAER), and those peptides with amino groups will be selectively and covalently captured. Release of the peptides on hydrolysis with trifluoroacetic acid (TFA) results in peptides that have a 4-formyl-benzamido group where the nitro group used to be. In qualitative setups, the procedure can be used to identify proteins modified by reactive nitrogen species and to determine the specific sites of their nitration. Quantitative measurements can be performed by stable-isotope labeling of the peptides in the reductive dimethylation step. Preparation of the SPAER takes about 1 d. Enrichment of nitropeptides requires about 2 d, and sample preparations need 1-30 h, depending on the experimental design. LC-MS/MS assays take from 4 h to several days and data processing can be done in 1-7 d.
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Pan Y, Ye M, Zheng H, Cheng K, Sun Z, Liu F, Liu J, Wang K, Qin H, Zou H. Trypsin-Catalyzed N-Terminal Labeling of Peptides with Stable Isotope-Coded Affinity Tags for Proteome Analysis. Anal Chem 2014; 86:1170-7. [DOI: 10.1021/ac403060d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanbo Pan
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Zheng
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Sun
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjie Liu
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keyun Wang
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- Key
Laboratory of Separation Sciences for Analytical Chemistry, National
Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Song C, Wang F, Cheng K, Wei X, Bian Y, Wang K, Tan Y, Wang H, Ye M, Zou H. Large-Scale Quantification of Single Amino-Acid Variations by a Variation-Associated Database Search Strategy. J Proteome Res 2013; 13:241-8. [DOI: 10.1021/pr400544j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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, 457 Zhongshan Road, Dalian 116023, China
- SINOPEC Research Institute of Petroleum Processing, 18 Xueyuan Road, Beijing 100083, China
| | - 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, 457 Zhongshan Road, 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, 457 Zhongshan Road, Dalian 116023, China
| | - Xiaoluan Wei
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yexiong Tan
- The
International Cooperation Laboratory on Signal Transduction of Eastern
Hepatobiliary Surgery Institute, Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
| | - Hongyang Wang
- The
International Cooperation Laboratory on Signal Transduction of Eastern
Hepatobiliary Surgery Institute, Second Military Medical University, 225 Changhai Road, Shanghai 200438, 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, 457 Zhongshan Road, 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, 457 Zhongshan Road, Dalian 116023, China
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Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, Figeys D. Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Anal Chem 2013; 86:176-95. [DOI: 10.1021/ac403551f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Zhibin Ning
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Rui Chen
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Daniel Figeys
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
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Liu M, Zhang L, Zhang L, Yao J, Yang P, Lu H. Approach for Identification and Quantification of C-Terminal Peptides: Incorporation of Isotopic Arginine Labeling Based on Oxazolone Chemistry. Anal Chem 2013; 85:10745-53. [DOI: 10.1021/ac401647m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Minbo Liu
- Shanghai
Cancer Centre and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Lijuan Zhang
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Lei Zhang
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Jun Yao
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Pengyuan Yang
- Shanghai
Cancer Centre and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
| | - Haojie Lu
- Shanghai
Cancer Centre and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200433, P. R. China
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Halcsik E, Forni MF, Fujita A, Verano-Braga T, Jensen ON, Sogayar MC. New insights in osteogenic differentiation revealed by mass spectrometric assessment of phosphorylated substrates in murine skin mesenchymal cells. BMC Cell Biol 2013; 14:47. [PMID: 24148232 PMCID: PMC3819743 DOI: 10.1186/1471-2121-14-47] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 10/09/2013] [Indexed: 01/15/2023] Open
Abstract
Background Bone fractures and loss represent significant costs for the public health system and often affect the patients quality of life, therefore, understanding the molecular basis for bone regeneration is essential. Cytokines, such as IL-6, IL-10 and TNFα, secreted by inflammatory cells at the lesion site, at the very beginning of the repair process, act as chemotactic factors for mesenchymal stem cells, which proliferate and differentiate into osteoblasts through the autocrine and paracrine action of bone morphogenetic proteins (BMPs), mainly BMP-2. Although it is known that BMP-2 binds to ActRI/BMPR and activates the SMAD 1/5/8 downstream effectors, little is known about the intracellular mechanisms participating in osteoblastic differentiation. We assessed differences in the phosphorylation status of different cellular proteins upon BMP-2 osteogenic induction of isolated murine skin mesenchymal stem cells using Triplex Stable Isotope Dimethyl Labeling coupled with LC/MS. Results From 150 μg of starting material, 2,264 proteins were identified and quantified at five different time points, 235 of which are differentially phosphorylated. Kinase motif analysis showed that several substrates display phosphorylation sites for Casein Kinase, p38, CDK and JNK. Gene ontology analysis showed an increase in biological processes related with signaling and differentiation at early time points after BMP2 induction. Moreover, proteins involved in cytoskeleton rearrangement, Wnt and Ras pathways were found to be differentially phosphorylated during all timepoints studied. Conclusions Taken together, these data, allow new insights on the intracellular substrates which are phosphorylated early on during differentiation to BMP2-driven osteoblastic differentiation of skin-derived mesenchymal stem cells.
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Affiliation(s)
| | | | | | | | | | - Mari Cleide Sogayar
- Chemistry Institute, Department of Biochemistry, Cell and Molecular Therapy Center (NUCEL/NETCEM), School of Medicine, University of São Paulo, São Paulo 05508-000, SP, Brazil.
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Yin HR, Zhang L, Xie LQ, Huang LY, Xu Y, Cai SJ, Yang PY, Lu HJ. Hyperplex-MRM: A Hybrid Multiple Reaction Monitoring Method Using mTRAQ/iTRAQ Labeling for Multiplex Absolute Quantification of Human Colorectal Cancer Biomarker. J Proteome Res 2013; 12:3912-9. [DOI: 10.1021/pr4005025] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hong-Rui Yin
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Li-Qi Xie
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Li-Yong Huang
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Ye Xu
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - San-Jun Cai
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Peng-Yuan Yang
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Hao-Jie Lu
- Shanghai Cancer Center and Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
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Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 928:83-92. [DOI: 10.1016/j.jchromb.2013.03.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 03/22/2013] [Accepted: 03/24/2013] [Indexed: 12/26/2022]
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Krüger T, Lehmann T, Rhode H. Effect of quality characteristics of single sample preparation steps in the precision and coverage of proteomic studies—A review. Anal Chim Acta 2013; 776:1-10. [DOI: 10.1016/j.aca.2013.01.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 11/25/2022]
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Sui P, Watanabe H, Ossipov MH, Porreca F, Bakalkin G, Bergquist J, Artemenko K. Dimethyl-Labeling-Based Protein Quantification and Pathway Search: A Novel Method of Spinal Cord Analysis Applicable for Neurological Studies. J Proteome Res 2013; 12:2245-52. [DOI: 10.1021/pr4001064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | - Michael H. Ossipov
- Department of Pharmacology, University of Arizona Health Sciences Center, Tucson,
Arizona 85724, United States
| | - Frank Porreca
- Department of Pharmacology, University of Arizona Health Sciences Center, Tucson,
Arizona 85724, United States
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Wang F, Blanchard AP, Elisma F, Granger M, Xu H, Bennett SAL, Figeys D, Zou H. Phosphoproteome analysis of an early onset mouse model (TgCRND8) of Alzheimer's disease reveals temporal changes in neuronal and glia signaling pathways. Proteomics 2013; 13:1292-305. [DOI: 10.1002/pmic.201200415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 10/19/2012] [Accepted: 11/08/2012] [Indexed: 12/12/2022]
Affiliation(s)
- Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic R & A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian P. R. China
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
| | - Alexandre P. Blanchard
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Neural Regeneration Laboratory; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa Canada
| | - Fred Elisma
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
| | - Matthew Granger
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Neural Regeneration Laboratory; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa Canada
| | - Hongbin Xu
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Neural Regeneration Laboratory; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa Canada
| | - Steffany A. L. Bennett
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Neural Regeneration Laboratory; Department of Biochemistry, Microbiology, and Immunology; University of Ottawa; Ottawa Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
| | - Hanfa Zou
- Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic R & A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian P. R. China
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46
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Analysis of human serum phosphopeptidome by a focused database searching strategy. J Proteomics 2013; 78:389-97. [DOI: 10.1016/j.jprot.2012.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/17/2012] [Accepted: 10/08/2012] [Indexed: 12/20/2022]
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47
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Wang X, Bian Y, Cheng K, Gu LF, Ye M, Zou H, Sun SSM, He JX. A large-scale protein phosphorylation analysis reveals novel phosphorylation motifs and phosphoregulatory networks in Arabidopsis. J Proteomics 2012; 78:486-98. [PMID: 23111157 DOI: 10.1016/j.jprot.2012.10.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/10/2012] [Accepted: 10/19/2012] [Indexed: 01/08/2023]
Abstract
Large-scale protein phosphorylation analysis by MS is emerging as a powerful tool in plant signal transduction research. However, our current understanding of the phosphorylation regulatory network in plants is still very limited. Here, we report on a proteome-wide profiling of phosphopeptides in nine-day-old Arabidopsis (Arabidopsis thaliana) seedlings by using an enrichment method combining the titanium (Ti(4+))-based IMAC and the RP-strong cation exchange (RP-SCX) biphasic trap column-based online RPLC. Through the duplicated RPLC-MS/MS analyses, we identified 5348 unique phosphopeptides for 2552 unique proteins. Among the phosphoproteins identified, 41% of them were first-time identified. Further evolutionary conservation and phosphorylation motif analyses of the phosphorylation sites discovered 100 highly conserved phosphorylation residues and identified 17 known and 14 novel motifs specific for Ser/Thr protein kinases. Gene ontology and pathway analyses revealed that many of the new identified phosphoproteins are important regulatory proteins that are involved in diverse biological processes, particularly in central metabolisms and cell signaling. Taken together, our results provided not only new insights into the complex phosphoregulatory network in plants but also important resources for future functional studies of protein phosphorylation in plant growth and development.
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Affiliation(s)
- Xu Wang
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
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48
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Wang F, Wei X, Zhou H, Liu J, Figeys D, Zou H. Combination of online enzyme digestion with stable isotope labeling for high-throughput quantitative proteome analysis. Proteomics 2012; 12:3129-37. [DOI: 10.1002/pmic.201200162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/15/2012] [Accepted: 08/14/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Xiaoluan Wei
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Hu Zhou
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jing Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
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49
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Zhang Z, Wang F, Xu B, Qin H, Ye M, Zou H. Preparation of capillary hybrid monolithic column with sulfonate strong cation exchanger for proteome analysis. J Chromatogr A 2012; 1256:136-43. [DOI: 10.1016/j.chroma.2012.07.071] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/16/2022]
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50
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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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