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Rejeeth C, Sharma A. Label-free designed nanomaterials enrichment and separation techniques for phosphoproteomics based on mass spectrometry. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.1047055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The surface chemical characteristics of nanomaterials have a substantial impact on the affinity probe used to enrich proteins and peptides for MALDI-MS analysis of a real human sample. Detecting phosphoproteins involved in signalling is always difficult, even with recent developments in mass spectrometry, because protein phosphorylation is often temporary from complicated mixtures. This review summarizes current research on the successful enrichment of various intriguing glycoproteins and glycol peptides using surface affinity materials with distinctive qualities such as low cost, excellent structural stability, diversity, and multifunction. As a consequence, this review will provide a quick overview of the scholars from various backgrounds who are working in this intriguing interdisciplinary field. Label-free cancer biomarkers and other diseases will benefit from future challenges.
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Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics 2021; 18:795-807. [PMID: 34652972 DOI: 10.1080/14789450.2021.1994390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Protein phosphorylation is a primary mechanism of signal transduction in cellular systems. Isobaric tagging can be used to investigate alterations in phosphorylation events in sample multiplexing experiments where quantification extends across all conditions. As such, innovations in tandem mass tag methods can facilitate the expansion of the depth and breadth of phosphoproteomic analyses. AREAS COVERED This review discusses the current state of tandem mass tag-centric phosphoproteomics and highlights advances in reagent chemistry, instrumentation, data acquisition, and data analysis. We stress that approaches for phosphoproteomic investigations require high-specificity enrichment, sensitive detection, and accurate phosphorylation site localization. EXPERT OPINION Tandem mass tag-centric phosphoproteomics will continue to be an important conduit for our understanding of signal transduction in living organisms. We anticipate that progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in analytical strategies will be key to the discovery of biologically relevant findings from phosphoproteomics studies.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
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3
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Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics 2021; 21:e2000140. [PMID: 33455035 DOI: 10.1002/pmic.202000140] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
Eukaryotic protein phosphorylation modulates nearly every major biological process. Phosphorylation regulates protein activity, mediates cellular signal transduction, and manipulates cellular structure. Consequently, the dysregulation of kinase and phosphatase pathways has been linked to a multitude of diseases. Mass spectrometry-based proteomic techniques are increasingly used for the global interrogation of perturbations in phosphorylation-based cellular signaling. Strategies for studying phosphoproteomes require high-specificity enrichment, sensitive detection, and accurate localization of phosphorylation sites with advanced LC-MS/MS techniques and downstream informatics. Sample multiplexing with isobaric tags has also been integral to recent advancements in throughput and sensitivity for phosphoproteomic studies. Each of these facets of phosphoproteomics analysis present distinct challenges and thus opportunities for improvement and innovation. Here, we review current methodologies, explore persistent challenges, and discuss the outlook for isobaric tag-based quantitative phosphoproteomic analysis.
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Affiliation(s)
- Joao A Paulo
- Harvard Medical School, Boston, Massachusetts, USA
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4
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Xiao J, Yang SS, Wu JX, Wu N, Yu X, Shang W, Gu ZY. Sn-based metal-organic framework for highly selective capture of monophosphopeptides. Talanta 2021; 224:121812. [PMID: 33379037 DOI: 10.1016/j.talanta.2020.121812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 11/28/2022]
Abstract
Sn-based metal-organic framework (MOF) was utilized to effectively capture monophosphopeptides due to the unique affinity. The Sn-based MOF demonstrated the good sensitivity and selectivity in the model phosphoproteins enrichment and was successfully applied in the biological fluids.
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Affiliation(s)
- Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jian-Xiang Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Nan Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China.
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Sugiyama N. Mass Spectrometry-Based Discovery of in vitro Kinome Substrates. ACTA ACUST UNITED AC 2020; 9:A0082. [PMID: 32547896 PMCID: PMC7242781 DOI: 10.5702/massspectrometry.a0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/10/2020] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation mediated by protein kinases is one of the most significant posttranslational modifications in many biological events. The function and physiological substrates of specific protein kinases, which are highly associated with known signal transduction elements or therapeutic targets, have been extensively studied using various approaches; however, most protein kinases have not yet been characterized. In recent decades, many techniques have been developed for the identification of in vitro and physiological substrates of protein kinases. In this review, I summarize recent studies profiling the characteristics of kinases using mass spectrometry-based proteomics, focusing on the large-scale identification of in vitro substrates of the human kinome using a quantitative phosphoproteomics approach.
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Affiliation(s)
- Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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6
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Li JY, Cao ZM, Hua Y, Wei G, Yu XZ, Shang WB, Lian HZ. Solvothermal Synthesis of Novel Magnetic Nickel Based Iron Oxide Nanocomposites for Selective Capture of Global- and Mono-Phosphopeptides. Anal Chem 2019; 92:1058-1067. [DOI: 10.1021/acs.analchem.9b04053] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jia-yuan Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhao-ming Cao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Yu Hua
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Gao Wei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Xi-zhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wen-bin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hong-zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
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7
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Affiliation(s)
- Yasushi ISHIHAMA
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University
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8
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Sugiyama N, Ishihama Y. Large-scale profiling of protein kinases for cellular signaling studies by mass spectrometry and other techniques. J Pharm Biomed Anal 2016; 130:264-272. [DOI: 10.1016/j.jpba.2016.05.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 01/26/2023]
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Ramalingam A, Kudapa H, Pazhamala LT, Weckwerth W, Varshney RK. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:1116. [PMID: 26734026 PMCID: PMC4689856 DOI: 10.3389/fpls.2015.01116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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11
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Svane S, Jørgensen TJD, McKenzie CJ, Kjeldsen F. Effect of Metals in Biomimetic Dimetal Complexes on Affinity and Gas-Phase Protection of Phosphate Esters. Anal Chem 2015; 87:7060-8. [DOI: 10.1021/acs.analchem.5b00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Svane
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Thomas J. D. Jørgensen
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Christine J. McKenzie
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
| | - Frank Kjeldsen
- Department of Biochemistry
and Molecular Biology, and ‡Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, 5230, Odense M, Denmark
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12
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Shi T, Gao Y, Gaffrey MJ, Nicora CD, Fillmore TL, Chrisler WB, Gritsenko MA, Wu C, He J, Bloodsworth KJ, Zhao R, Camp DG, Liu T, Rodland KD, Smith RD, Wiley HS, Qian WJ. Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment. Anal Chem 2014; 87:1103-10. [PMID: 25517423 DOI: 10.1021/ac503797x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Targeted mass spectrometry is a promising technology for site-specific quantification of posttranslational modifications. However, a major constraint is the limited sensitivity for quantifying low-abundance PTMs, requiring the use of affinity reagents for enrichment. Herein, we demonstrate the direct site-specific quantification of ERK phosphorylation isoforms (pT, pY, pTpY) and their relative stoichiometry using a sensitive targeted MS approach termed high-pressure, high-resolution separations with intelligent selection, and multiplexing (PRISM). PRISM provides effective enrichment of target peptides into a given fraction from complex mixture, followed by selected reaction monitoring quantification. Direct quantification of ERK phosphorylation in human mammary epithelial cells (HMEC) was demonstrated from as little as 25 μg tryptic peptides from whole cell lysates. Compared to immobilized metal-ion affinity chromatography, PRISM provided ∼10-fold higher signal intensities, presumably due to the better peptide recovery of PRISM. This approach was applied to quantify ERK phosphorylation dynamics in HMEC treated by different doses of epidermal growth factor at both the peak activation (10 min) and steady state (2 h). The maximal ERK activation was observed with 0.3 and 3 ng/mL doses for 10 min and 2 h time points, respectively. The dose-response profiles of individual phosphorylated isoforms showed that singly phosphorylated pT-ERK never increases significantly, while the increase of pY-ERK paralleled that of pTpY-ERK. This data supports for a processive, rather than distributed model of ERK phosphorylation. The PRISM-SRM quantification of protein phosphorylation illustrates the potential for simultaneous quantification of multiple PTMs.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99354, United States
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13
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [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: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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14
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Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S. Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns. Mol Cell Proteomics 2014; 14:205-15. [PMID: 25394399 DOI: 10.1074/mcp.m114.043109] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Advances in phosphopeptide enrichment methods enable the identification of thousands of phosphopeptides from complex samples. Current offline enrichment approaches using TiO(2), Ti, and Fe immobilized metal ion affinity chromatography (IMAC) material in batch or microtip format are widely used, but they suffer from irreproducibility and compromised selectivity. To address these shortcomings, we revisited the merits of performing phosphopeptide enrichment in an HPLC column format. We found that Fe-IMAC columns enabled the selective, comprehensive, and reproducible enrichment of phosphopeptides out of complex lysates. Column enrichment did not suffer from bead-to-sample ratio issues and scaled linearly from 100 μg to 5 mg of digest. Direct measurements on an Orbitrap Velos mass spectrometer identified >7500 unique phosphopeptides with 90% selectivity and good quantitative reproducibility (median cv of 15%). The number of unique phosphopeptides could be increased to more than 14,000 when the IMAC eluate was subjected to a subsequent hydrophilic strong anion exchange separation. Fe-IMAC columns outperformed Ti-IMAC and TiO(2) in batch or tip mode in terms of phosphopeptide identification and intensity. Permutation enrichments of flow-throughs showed that all materials largely bound the same phosphopeptide species, independent of physicochemical characteristics. However, binding capacity and elution efficiency did profoundly differ among the enrichment materials and formats. As a result, the often quoted orthogonality of the materials has to be called into question. Our results strongly suggest that insufficient capacity, inefficient elution, and the stochastic nature of data-dependent acquisition in mass spectrometry are the causes of the experimentally observed complementarity. The Fe-IMAC enrichment workflow using an HPLC format developed here enables rapid and comprehensive phosphoproteome analysis that can be applied to a wide range of biological systems.
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Affiliation(s)
- Benjamin Ruprecht
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany, ¶ Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Heiner Koch
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Guillaume Medard
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Max Mundt
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany, ¶ Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
| | - Simone Lemeer
- From the * Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany, ¶ Center for Integrated Protein Science Munich, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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15
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Yu Q, Li XS, Yuan BF, Feng YQ. Preparation of magnetic hydroxyapatite clusters and their application in the enrichment of phosphopeptides. J Sep Sci 2014; 37:580-6. [DOI: 10.1002/jssc.201301241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/05/2013] [Accepted: 12/06/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Qiao Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education); Department of Chemistry; Wuhan University; Wuhan P. R. China
| | - Xiao-Shui Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education); Department of Chemistry; Wuhan University; Wuhan P. R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education); Department of Chemistry; Wuhan University; Wuhan P. R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education); Department of Chemistry; Wuhan University; Wuhan P. R. China
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16
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Wakabayashi M, Yoshihara H, Masuda T, Tsukahara M, Sugiyama N, Ishihama Y. Phosphoproteome Analysis of Formalin-Fixed and Paraffin-Embedded Tissue Sections Mounted on Microscope Slides. J Proteome Res 2013; 13:915-24. [DOI: 10.1021/pr400960r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Masaki Wakabayashi
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroki Yoshihara
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
| | - Takeshi Masuda
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
| | - Mai Tsukahara
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
| | - Yasushi Ishihama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Institute
for Advanced Biosciences, Keio University, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
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17
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Wu CC, Han CC, Chang HC. Applications of Surface-Functionalized Diamond Nanoparticles for Mass-Spectrometry-Based Proteomics. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Zheng L, Dong H, Hu L. Zirconium-Cation-Immobilized Core/Shell (Fe3O4@Polymer) Microspheres as an IMAC Material for the Selective Enrichment of Phosphopeptides. Ind Eng Chem Res 2013. [DOI: 10.1021/ie4003377] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leyou Zheng
- NHU Co. Ltd. of Zhejiang, 4 Jiangbei Road,
Xinchang, Zhejiang 312500, P. R. China
| | - Huaping Dong
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing,
Zhejiang 312000, P. R. China
| | - Liujiang Hu
- College of Chemistry and Chemical Engineering, Shaoxing University, 508 Huancheng West Road, Shaoxing,
Zhejiang 312000, P. R. China
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19
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Qu Y, Wu S, Zhao R, Zink E, Orton DJ, Moore RJ, Meng D, Clauss TRW, Aldrich JT, Lipton MS, Paša-Tolić L. Automated immobilized metal affinity chromatography system for enrichment of Escherichia coli phosphoproteome. Electrophoresis 2013; 34:1619-26. [PMID: 23494780 DOI: 10.1002/elps.201200628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/01/2013] [Accepted: 02/15/2013] [Indexed: 11/09/2022]
Abstract
Enrichment of bacterial phosphopeptides is an essential step prior to bottom-up mass spectrometry-based analysis of the phosphoproteome, which is fundamental to understanding the role of phosphoproteins in cell signaling and regulation of protein activity. We developed an automated immobilized metal affinity chromatography (IMAC) system to enrich strong cation exchange-fractionated phosphopeptides from the soluble proteome of Escherichia coli MG1655 grown on minimal medium. Initial demonstration of the system resulted in identification of 75 phosphopeptides covering 52 phosphoproteins. Consistent with previous studies, many of these phosphoproteins are involved in the carbohydrate portion of central metabolism. The automated system utilizes a large capacity IMAC column that can effectively enrich phosphopeptides from a bacterial sample by increasing peptide loading and reducing the wash time. An additional benefit of the automated IMAC system is reduced labor and associated costs.
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Affiliation(s)
- Yi Qu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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Zhang Y, Li L, Ma W, Zhang Y, Yu M, Guo J, Lu H, Wang C. Two-in-one strategy for effective enrichment of phosphopeptides using magnetic mesoporous γ-Fe₂O₃ nanocrystal clusters. ACS APPLIED MATERIALS & INTERFACES 2013; 5:614-621. [PMID: 23294124 DOI: 10.1021/am3019806] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Designed with a two-in-one strategy, the magnetic mesoporous γ-Fe(2)O(3) nanocrystal clusters (m-γ-Fe(2)O(3)) have been successfully prepared for integrating the functions of effective enrichment and quick separation of phosphopeptides into a single architecture. First, the mesoporous Fe(3)O(4) nanocrystal clusters (mFe(3)O(4)) were synthesized by solvothermal reaction and then were subjected to calcination in air to form m-γ-Fe(2)O(3). The obtained m-γ-Fe(2)O(3) have spherical morphology with uniform particle size of about 200 nm and mesoporous structure with the pore diameter of about 9.7 nm; the surface area is as large as 117.8 m(2)/g, and the pore volume is 0.34 cm(3)/g. The m-γ-Fe(2)O(3) possessed very high magnetic responsiveness (Ms = 78.8 emu/g, magnetic separation time from solution is less than 5 s) and were used for the selective enrichment of phosphopeptides for the first time. The experimental results demonstrated that the m-γ-Fe(2)O(3) possessed high selectivity for phosphopeptides at a low molar ratio of phosphopeptides/nonphosphopeptides (1:100), high sensitivity (the detection limit was at the fmol level), high enrichment recovery (as high as 89.4%), and excellent speed (the enrichment can be completed in 10 min). Moreover, this material is also quite effective for enrichment of phosphopeptides from the real sample (drinking milk), showing great potential in the practical application.
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Affiliation(s)
- Yuting Zhang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
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21
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Li QR, Ning ZB, Yang XL, Wu JR, Zeng R. Complementary workflow for global phosphoproteome analysis. Electrophoresis 2012; 33:3291-8. [DOI: 10.1002/elps.201200124] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 07/26/2012] [Accepted: 09/05/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Qing-Run Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Zhi-Bin Ning
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Xing-Lin Yang
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Jia-Rui Wu
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai; China
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22
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Imamura H, Wakabayashi M, Ishihama Y. Analytical strategies for shotgun phosphoproteomics: Status and prospects. Semin Cell Dev Biol 2012; 23:836-42. [DOI: 10.1016/j.semcdb.2012.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/29/2012] [Indexed: 12/17/2022]
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Meyer LJ, Gao J, Xu D, Thelen JJ. Phosphoproteomic analysis of seed maturation in Arabidopsis, rapeseed, and soybean. PLANT PHYSIOLOGY 2012; 159:517-28. [PMID: 22440515 PMCID: PMC3375983 DOI: 10.1104/pp.111.191700] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 03/19/2012] [Indexed: 05/03/2023]
Abstract
To characterize protein phosphorylation in developing seed, a large-scale, mass spectrometry-based phosphoproteomic study was performed on whole seeds at five sequential stages of development in soybean (Glycine max), rapeseed (Brassica napus), and Arabidopsis (Arabidopsis thaliana). Phosphopeptides were enriched from 0.5 mg of total peptides using a combined strategy of immobilized metal affinity and metal oxide affinity chromatography. Enriched phosphopeptides were analyzed by Orbitrap tandem mass spectrometry and mass spectra mined against cognate genome or cDNA databases in both forward and randomized orientations, the latter to calculate false discovery rate. We identified a total of 2,001 phosphopeptides containing 1,026 unambiguous phosphorylation sites from 956 proteins, with an average false discovery rate of 0.78% for the entire study. The entire data set was uploaded into the Plant Protein Phosphorylation Database (www.p3db.org), including all meta-data and annotated spectra. The Plant Protein Phosphorylation Database is a portal for all plant phosphorylation data and allows for homology-based querying of experimentally determined phosphosites. Comparisons with other large-scale phosphoproteomic studies determined that 652 of the phosphoproteins are novel to this study. The unique proteins fall into several Gene Ontology categories, some of which are overrepresented in our study as well as other large-scale phosphoproteomic studies, including metabolic process and RNA binding; other categories are only overrepresented in our study, like embryonic development. This investigation shows the importance of analyzing multiple plants and plant organs to comprehensively map the complete plant phosphoproteome.
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Affiliation(s)
- Louis J. Meyer
- Department of Biochemistry (L.J.M., J.J.T.) and Department of Computer Sciences (J.G., D.X.), Christopher S. Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Jianjiong Gao
- Department of Biochemistry (L.J.M., J.J.T.) and Department of Computer Sciences (J.G., D.X.), Christopher S. Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Dong Xu
- Department of Biochemistry (L.J.M., J.J.T.) and Department of Computer Sciences (J.G., D.X.), Christopher S. Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Jay J. Thelen
- Department of Biochemistry (L.J.M., J.J.T.) and Department of Computer Sciences (J.G., D.X.), Christopher S. Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
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Cardoza JD, Parikh JR, Ficarro SB, Marto JA. Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2012; 4:141-62. [PMID: 22231900 PMCID: PMC3288153 DOI: 10.1002/wsbm.166] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mass spectrometry has become the method of choice for proteome characterization, including multicomponent protein complexes (typically tens to hundreds of proteins) and total protein expression (up to tens of thousands of proteins), in biological samples. Qualitative sequence assignment based on MS/MS spectra is relatively well-defined, while statistical metrics for relative quantification have not completely stabilized. Nonetheless, proteomics studies have progressed to the point whereby various gene-, pathway-, or network-oriented computational frameworks may be used to place mass spectrometry data into biological context. Despite this progress, the dynamic range of protein expression remains a significant hurdle, and impedes comprehensive proteome analysis. Methods designed to enrich specific protein classes have emerged as an effective means to characterize enzymes or other catalytically active proteins that are otherwise difficult to detect in typical discovery mode proteomics experiments. Collectively, these approaches will facilitate identification of biomarkers and pathways relevant to diagnosis and treatment of human disease.
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Affiliation(s)
- Job D. Cardoza
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Jignesh R. Parikh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Bioinformatics Program, Boston University, Boston, MA 02115
| | - Scott B. Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Jarrod A. Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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25
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Zeng YY, Chen HJ, Shiau KJ, Hung SU, Wang YS, Wu CC. Efficient enrichment of phosphopeptides by magnetic TiO₂-coated carbon-encapsulated iron nanoparticles. Proteomics 2012; 12:380-90. [PMID: 22144111 DOI: 10.1002/pmic.201000726] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 10/31/2011] [Accepted: 11/14/2011] [Indexed: 01/17/2023]
Abstract
Titanium dioxide (TiO₂) has been widely used for phosphopeptide enrichment. Several approaches have been reported to produce magnetic TiO₂ affinity probes. In this report, we present a facile approach to immobilize TiO₂ onto poly(acrylic acid)-functionalized magnetic carbon-encapsulated iron nanoparticles as affinity probes for efficient enrichment of phosphopeptides. By using the new magnetic TiO₂ affinity probes, denoted as TiO₂-coated Fe@CNPs, rapid and effective MALDI-TOF MS profiling of phosphopeptides was demonstrated in different model systems such as tryptic digests of β-casein, and complex β-casein/BSA mixture. The TiO₂-coated Fe@CNPs out-performed the commercial TiO₂-coated magnetic beads for detection of phosphopeptides from tryptic digests of β-casein/BSA mixture with a molar ratio of 1:100. The new TiO₂-coated magnetic probes were also proven to be applicable for real life samples. The magnetic TiO₂-coated Fe@CNPs were employed to selectively isolate phosphopeptides from tryptic digests of HeLa cell lysates and out-performed the commercial magnetic TiO₂ beads in the number of identified phosphopeptides and phosphorylation sites. In a 200-μg equivalent of HeLa cell lysates, we identified 1415 unique phosphopeptides and 1093 phosphorylation sites, indicating the good performance of the new approach.
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Affiliation(s)
- Yi Y Zeng
- Department of Applied Chemistry, National Chi Nan University, Puli, Nantou, Taiwan
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Li XS, Xu LD, Zhu GT, Yuan BF, Feng YQ. Zirconium arsenate-modified magnetic nanoparticles: preparation, characterization and application to the enrichment of phosphopeptides. Analyst 2012; 137:959-67. [DOI: 10.1039/c2an15985f] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Luckey CJ, Lu Y, Marto JA. Understanding the first steps in embryonic stem cell exit from the pluripotent state. Transfusion 2011; 51 Suppl 4:118S-124S. [PMID: 22074622 DOI: 10.1111/j.1537-2995.2011.03374.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND We are interested in understanding how a given cell type, in response to external cues from its environment, makes the decision to differentiate. In the case of mouse embryonic stem cells (mESCs), the key external factor that maintains their undifferentiated state is the cytokine leukemia inhibitory factor (LIF). LIF removal causes mESCs to exit their pluripotent state and differentiate into more restricted precursors. Although LIF is known to activate multiple different phosphorylation cascades, the mechanisms by which its removal leads to mESC differentiation are not well understood. STUDY DESIGN AND METHODS In order to identify the molecular events that occur upon LIF removal, we developed a set of novel experimental approaches that allowed identification and quantification of global phosphorylation changes that occur when mESCs are deprived of LIF. These included growth of mESCs on permeable membranes and development of a robust and sensitive phospho-proteomics platform to quantify early signaling events. RESULTS In addition to the well-characterized tyrosine 705 phosphorylation of STAT3, LIF removal results in the rapid phosphorylation of multiple other proteins known to regulate the mESC self-renewal on both tyrosine, serine, and threonine residues. We hypothesize that these unique posttranslational modifications help drive the exit of mESCs from the pluripotent state. CONCLUSIONS Our data set the stage for future studies investigating the functional role of these phosphorylation events in mESCs. These studies were greatly facilitated by the National Blood Foundation, whose support in the crucial initiation phase of these studies was invaluable.
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Affiliation(s)
- C John Luckey
- Department of Pathology, Brigham and Women's Hospital, Joint Program in Transfusion Medicine, Department of Cancer Biology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, Massachusetts 02115, USA.
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Chen CJ, Chen WY, Tseng MC, Chen YR. Tunnel frit: a nonmetallic in-capillary frit for nanoflow ultra high-performance liquid chromatography-mass spectrometryapplications. Anal Chem 2011; 84:297-303. [PMID: 22097963 DOI: 10.1021/ac202549y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this study, an easy method to fabricate a durable in-capillary frit was developed for use in nanoflow liquid chromatography (nanoLC). A small orifice was tunneled into the sol-gel frit during the polymerization process resulting in the simple fabrication of a tunnel frit. A short packing tunnel frit column (2 cm, C(18) particles) was able to sustain over 10,000 psi continuous liquid flow for 10 days without observation of particle loss, and back pressure variation was less than 5%. The tunnel frit was successfully applied to the fabrication of nanoflow ultra high-performance liquid chromatography (nano-UHPLC) trap and analytical columns. In the analysis of tryptic peptides, the tunnel frit trap and analytical columns were demonstrated to have high separation efficiency and sensitivity. In analysis of phosphopeptides, the use of the nonmetallic tunnel frit column showed better sensitivity than the metallic frit column. This design can facilitate the preparation of nano-HPLC and nano-UHPLC columns and the packing material can easily be refilled when the column is severely contaminated or clogged.
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Affiliation(s)
- Chao-Jung Chen
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404, Taiwan
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29
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Bridon G, Bonneil E, Muratore-Schroeder T, Caron-Lizotte O, Thibault P. Improvement of Phosphoproteome Analyses Using FAIMS and Decision Tree Fragmentation. Application to the Insulin Signaling Pathway in Drosophila melanogaster S2 Cells. J Proteome Res 2011; 11:927-40. [DOI: 10.1021/pr200722s] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | | | | | | | - Pierre Thibault
- Department of Chemistry, Université de Montréal, Montréal, Québec, Canada H3C 3J7
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30
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Fíla J, Honys D. Enrichment techniques employed in phosphoproteomics. Amino Acids 2011; 43:1025-47. [PMID: 22002794 PMCID: PMC3418503 DOI: 10.1007/s00726-011-1111-z] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 09/26/2011] [Indexed: 11/28/2022]
Abstract
Rapid changes of protein phosphorylation play a crucial role in the regulation of many cellular processes. Being post-translationally modified, phosphoproteins are often present in quite low abundance and tend to co-exist with their unphosphorylated isoform within the cell. To make their identification more practicable, the use of enrichment protocols is often required. The enrichment strategies can be performed either at the level of phosphoproteins or at the level of phosphopeptides. Both approaches have their advantages and disadvantages. Most enriching strategies are based on chemical modifications, affinity chromatography to capture peptides and proteins containing negatively charged phosphate groups onto a positively charged matrix, or immunoprecipitation by phospho-specific antibodies. In this article, the most up-to-date enrichment techniques are discussed, taking into account their optimization, and highlighting their advantages and disadvantages. Moreover, these methods are compared to each other, revealing their complementary nature in providing comprehensive coverage of the phosphoproteome.
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Affiliation(s)
- Jan Fíla
- Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague 6, Czech Republic
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31
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Lee DH, Chowdhury D. What goes on must come off: phosphatases gate-crash the DNA damage response. Trends Biochem Sci 2011; 36:569-77. [PMID: 21930385 DOI: 10.1016/j.tibs.2011.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 12/24/2022]
Abstract
DNA-damage-induced phospho-signaling has been studied for decades, with a focus mainly on initiation of the signaling cascade, and the kinases activated by DNA lesions. It is widely accepted that the balance of phosphorylation needs to be restored and/or maintained by phosphatases, yet there have only been sporadic efforts to investigate the impact of phosphatases on DNA repair. Recent advances in phosphoproteomic strategies and implementation of large genetic screens indicate that these enzymes play pivotal roles in these signaling networks. Dephosphorylation of repair proteins is crucial for efficient DNA repair, and the recommencement of cell division post-repair. Here, we focus on serine/threonine phosphatases implicated in dephosphorylation of DNA repair factors, summarizing recent findings and speculating on untested roles of phosphatases in the DNA damage response.
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Affiliation(s)
- Dong-Hyun Lee
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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Choi H, Lee S, Jun CD, Park ZY. Development of an off-line capillary column IMAC phosphopeptide enrichment method for label-free phosphorylation relative quantification. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:2991-7. [PMID: 21930439 DOI: 10.1016/j.jchromb.2011.08.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/29/2011] [Accepted: 08/24/2011] [Indexed: 11/26/2022]
Abstract
Immobilized metal affinity chromatography (IMAC) and metal oxide type affinity chromatography (MOAC) techniques have been widely used for mass spectrometry-based phosphorylation analysis. Unlike MOAC techniques, IMAC requires rather complete removals of buffering reagents, salts and high concentrations of denaturant prior to sample loading in order for the successful enrichment of phosphopeptides. In this study, a simple off-line capillary column-based IMAC phosphopeptide enrichment method can shorten sample preparation time by eliminating the speed-vac step from the desalting process. Tryptic digest peptide samples containing 2M urea can be directly processed and the entire IMAC procedure can be completed within 6 h. When tryptic digest peptide samples prepared from mouse whole brain tissues were analyzed using our method, an average of 249 phosphoproteins and 463 unique phosphopeptides were identified from single 2-h RPLC-MS/MS analysis (~88% specificity). An additional advantage of this method is the significantly improved reproducibility of the phosphopeptide enrichment results. When four independent phosphopeptide enrichment experiments were carried out, the peak areas of phosphopeptides identified among four enrichment experiments were relatively similar (less than 16.2% relative standard dev.). Because of this increased reproducibility, relative phosphorylation quantification analysis of major phosphoproteins appears to be feasible without the need for stable isotope labeling techniques.
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Affiliation(s)
- Hyunwoo Choi
- School of Life Sciences, Gwangju Institute of Science & Technology, 1 Oryong-Dong, Buk-Gu, Gwangju 500-712, Republic of Korea
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Mithoe SC, Menke FLH. Phosphoproteomics perspective on plant signal transduction and tyrosine phosphorylation. PHYTOCHEMISTRY 2011; 72:997-1006. [PMID: 21315387 DOI: 10.1016/j.phytochem.2010.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/25/2010] [Accepted: 12/06/2010] [Indexed: 05/14/2023]
Abstract
Plants and animal cells use intricate signaling pathways to respond to a diverse array of stimuli. These stimuli include signals from environment, such as biotic and abiotic stress signals, as well as cell-to-cell signaling required for pattern formation during development. The transduction of the signal often relies on the post-translational modification (PTM) of proteins. Protein phosphorylation in eukaryotic cells is considered to be a central mechanism for regulation and cellular signaling. The classic view is that phosphorylation of serine (Ser) and threonine (Thr) residues is more abundant, whereas tyrosine (Tyr) phosphorylation is less frequent. This review provides an overview of the progress in the plant phosphoproteomics field and how this progress has lead to a re-evaluation of the relative contribution of tyrosine phosphorylation to the plant phosphoproteome. In relation to this appreciated contribution of tyrosine phosphorylation we also discuss some of the recent progress on the role of tyrosine phosphorylation in plant signal transduction.
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Affiliation(s)
- Sharon C Mithoe
- Department of Biology, Molecular Genetics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Palumbo AM, Smith SA, Kalcic CL, Dantus M, Stemmer PM, Reid GE. Tandem mass spectrometry strategies for phosphoproteome analysis. MASS SPECTROMETRY REVIEWS 2011; 30:600-25. [PMID: 21294150 DOI: 10.1002/mas.20310] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.
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Affiliation(s)
- Amanda M Palumbo
- Department of Chemistry, Michigan State University, East Lansing, USA
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Wang H, Duan J, Xu H, Zhao L, Liang Y, Shan Y, Zhang L, Liang Z, Zhang Y. Monoliths with immobilized zirconium ions for selective enrichment of phosphopeptides. J Sep Sci 2011; 34:2113-21. [DOI: 10.1002/jssc.201100168] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/10/2011] [Accepted: 04/11/2011] [Indexed: 11/11/2022]
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Wu HT, Hsu CC, Tsai CF, Lin PC, Lin CC, Chen YJ. Nanoprobe-based immobilized metal affinity chromatography for sensitive and complementary enrichment of multiply phosphorylated peptides. Proteomics 2011; 11:2639-53. [PMID: 21630456 DOI: 10.1002/pmic.201000768] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/03/2011] [Accepted: 03/28/2011] [Indexed: 12/26/2022]
Abstract
Magnetic nanoparticles (MNP, <100 nm) have rapidly evolved as sensitive affinity probes for phosphopeptide enrichment. By taking advantage of the easy magnetic separation and flexible surface modification of the MNP, we developed a surface-blocked, nanoprobe-based immobilized metal ion affinity chromatography (NB-IMAC) method for the enhanced purification of multiply phosphorylated peptides. The NB-IMAC method allowed rapid and specific one-step enrichment by blocking the surface of titanium (IV) ion-charged nitrilotriacetic acid-conjugated MNP (Ti⁴-NTA-PEG@MNP) with low molecular weight polyethylene glycol. The MNP demonstrated highly sensitive and unbiased extraction of both mono- and multiply phosphorylated peptides from diluted β-casein (2 × 10⁻¹⁰ M). Without chemical derivation or fractionation, 1283 phosphopeptides were identified from 400 μg of Raji B cells with 80% purification specificity. We also showed the first systematic comparison on the particle size effect between nano-sclae IMAC and micro-scale IMAC. Inductively coupled plasma-mass spectrometry (ICP-MS) analysis revealed that MNP had a 4.6-fold higher capacity for metal ions per unit weight than did the magnetic micro-sized particle (MMP, 2-10 μm), resulting in the identification of more phosphopeptides as well as a higher percentage of multiply phosphorylated peptides (31%) at the proteome scale. Furthermore, NB-IMAC complements chromatography-based IMAC and TiO₂ methods because <13% of mono- and 12% of multiply phosphorylated peptide identifications overlapped among the 2700 phosphopeptides identified by the three methods. Notably, the number of multiply phosphorylated peptides was enriched twofold and threefold by NB-IMAC relative to micro-scale IMAC and TiO₂, respectively. NB-IMAC is an innovative material for increasing the identification coverage in phosphoproteomics.
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Affiliation(s)
- Huan-Ting Wu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
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Highly selective and sensitive enrichment of phosphopeptides via NiO nanoparticles using a microwave-assisted centrifugation on-particle ionization/enrichment approach in MALDI-MS. Anal Bioanal Chem 2011; 400:3451-62. [PMID: 21533801 DOI: 10.1007/s00216-011-5016-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/12/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
The strategy to concentrate phosphopeptides has become a critical issue for mapping protein phosphorylation sites, which are well known as posttranslational modifications in proteomics. In this study, we propose a simple and highly sensitive method for phosphopeptide enrichment on NiO nanoparticles (NPs) from a trypsin predigested phosphoprotein complex solution in a microwave oven. Furthermore, this technique was combined with centrifugation on-particle ionization/enrichment of phosphopeptides and phosphopeptides were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Weak magnetism of these NPs and a positive surface charge effect at low pH accomplished rapid and selective phosphopeptide enrichment within 30s. Trypsin-digested products of phosphoproteins such as α-casein and β-casein, human blood serum, nonfat milk, and egg white were also investigated to explore their phosphopeptide enrichment from complex samples by this approach. The results demonstrate that NiO NPs exhibit good affinity to trace the phosphopeptides even in the presence of 30 times higher molar concentration of complex solution of non-phosphopeptide proteolytic predigested bovine serum albumin. The detection limits of NiO NPs for α-casein and β-casein were 2.0 × 10(-9) M, with good signal-to-noise ratio in the mass spectrum. NiO NPs were found to be effective and selective for enrichment of singly and multiply phosphorylated peptides at a trace level in complex samples in a microwave oven. The cost of preparing NiO NPs is low, the NiO NPs are thermally stable, and therefore, they hold great promise for use in phosphopeptide enrichment.
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Hu Y, Peng Y, Lin K, Shen H, Brousseau LC, Sakamoto J, Sun T, Ferrari M. Surface engineering on mesoporous silica chips for enriching low molecular weight phosphorylated proteins. NANOSCALE 2011; 3:421-8. [PMID: 21135976 PMCID: PMC3397147 DOI: 10.1039/c0nr00720j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV=18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications.
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Affiliation(s)
- Ye Hu
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yang Peng
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kevin Lin
- Department of Biomedical Engineering, the University of Texas at Austin, Austin, TX, USA
| | - Haifa Shen
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Louis C. Brousseau
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jason Sakamoto
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Tong Sun
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mauro Ferrari
- Department of Nanomedicine and Biomedical Engineering, the University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Biomedical Engineering, the University of Texas at Austin, Austin, TX, USA
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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Chen CT, Wang LY, Ho YP. Use of polyethylenimine-modified magnetic nanoparticles for highly specific enrichment of phosphopeptides for mass spectrometric analysis. Anal Bioanal Chem 2011; 399:2795-806. [DOI: 10.1007/s00216-010-4623-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 11/25/2010] [Accepted: 12/17/2010] [Indexed: 10/18/2022]
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40
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Shiau KJ, Hung SU, Lee HW, Wu CC. Nanodiamond-based two-step sampling of multiply and singly phosphorylated peptides for MALDI-TOF mass spectrometry analysis. Analyst 2011; 136:1922-7. [DOI: 10.1039/c0an01046d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Trost M, Bridon G, Desjardins M, Thibault P. Subcellular phosphoproteomics. MASS SPECTROMETRY REVIEWS 2010; 29:962-90. [PMID: 20931658 DOI: 10.1002/mas.20297] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Protein phosphorylation represents one of the most extensively studied post-translational modifications, primarily due to the emergence of sensitive methods enabling the detection of this modification both in vitro and in vivo. The availability of enrichment methods combined with sensitive mass spectrometry instrumentation has played a crucial role in uncovering the dynamic changes and the large expanding repertoire of this reversible modification. The structural changes imparted by the phosphorylation of specific residues afford exquisite mechanisms for the regulation of protein functions by modulating new binding sites on scaffold proteins or by abrogating protein-protein interactions. However, the dynamic interplay of protein phosphorylation is not occurring randomly within the cell but is rather finely orchestrated by specific kinases and phosphatases that are unevenly distributed across subcellular compartments. This spatial separation not only regulates protein phosphorylation but can also control the activity of other enzymes and the transfer of other post-translational modifications. While numerous large-scale phosphoproteomics studies highlighted the extent and diversity of phosphoproteins present in total cell lysates, the further understanding of their regulation and biological activities require a spatio-temporal resolution only achievable through subcellular fractionation. This review presents a first account of the emerging field of subcellular phosphoproteomics where cell fractionation approaches are combined with sensitive mass spectrometry methods to facilitate the identification of low abundance proteins and to unravel the intricate regulation of protein phosphorylation.
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Affiliation(s)
- Matthias Trost
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
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42
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Ye J, Zhang X, Young C, Zhao X, Hao Q, Cheng L, Jensen ON. Optimized IMAC−IMAC Protocol for Phosphopeptide Recovery from Complex Biological Samples. J Proteome Res 2010; 9:3561-73. [DOI: 10.1021/pr100075x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juanying Ye
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Xumin Zhang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Clifford Young
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Xiaolu Zhao
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Qin Hao
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Lei Cheng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ole Nørregaard Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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The use of liquid phase deposition prepared phosphonate grafted silica nanoparticle-deposited capillaries in the enrichment of phosphopeptides. J Sep Sci 2010; 33:1806-15. [DOI: 10.1002/jssc.201000029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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44
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Ham BM, Jayachandran H, Yang F, Jaitly N, Polpitiya AD, Monroe ME, Wang L, Zhao R, Purvine SO, Livesay EA, Camp DG, Rossie S, Smith RD. Novel Ser/Thr protein phosphatase 5 (PP5) regulated targets during DNA damage identified by proteomics analysis. J Proteome Res 2010; 9:945-53. [PMID: 20039704 DOI: 10.1021/pr9008207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The DNA damage response likely includes a global phosphorylation signaling cascade process for sensing the damaged DNA condition and coordinating responses to cope with and repair the perturbed cellular state. We utilized a label-free liquid chromatography-mass spectrometry approach to evaluate changes in protein phosphorylation associated with PP5 activity during the DNA damage response. Biological replicate analyses of bleomycin-treated HeLa cells expressing either WT-PP5 or mutant inactive PP5 lead to the identification of six potential target proteins of PP5 action. Four of these putative targets have been previously reported to be involved in DNA damage responses. Using phospho-site specific antibodies, we confirmed that phosphorylation of one target, ribosomal protein S6, was selectively decreased in cells overexpressing catalytically inactive PP5. Our findings also suggest that PP5 may play a role in controlling translation and in regulating substrates for proline-directed kinases, such as MAP kinases and cyclin-dependent protein kinases that are involved in response to DNA damage.
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Affiliation(s)
- Bryan M Ham
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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45
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Ozlu N, Akten B, Timm W, Haseley N, Steen H, Steen JA. Phosphoproteomics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 2:255-276. [DOI: 10.1002/wsbm.41] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nurhan Ozlu
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bikem Akten
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Children's Hospital Boston, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Wiebke Timm
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Children's Hospital Boston, Boston, MA, USA
| | - Nathan Haseley
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Hanno Steen
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Children's Hospital Boston, Boston, MA, USA
| | - Judith A.J. Steen
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Children's Hospital Boston, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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46
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Argetsinger LS, Stuckey JA, Robertson SA, Koleva RI, Cline JM, Marto JA, Myers MG, Carter-Su C. Tyrosines 868, 966, and 972 in the kinase domain of JAK2 are autophosphorylated and required for maximal JAK2 kinase activity. Mol Endocrinol 2010; 24:1062-76. [PMID: 20304997 DOI: 10.1210/me.2009-0355] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Janus kinase 2 (JAK2) is activated by a majority of cytokine family receptors including receptors for GH, leptin, and erythropoietin. To identify novel JAK2-regulatory and/or -binding sites, we set out to identify autophosphorylation sites in the kinase domain of JAK2. Two-dimensional phosphopeptide mapping of in vitro autophosphorylated JAK2 identified tyrosines 868, 966, and 972 as sites of autophosphorylation. Phosphorylated tyrosines 868 and 972 were also identified by mass spectrometry analysis of JAK2 activated by an erythropoietin-bound chimeric erythropoietin receptor/leptin receptor. Phosphospecific antibodies suggest that the phosphorylation of all three tyrosines increases in response to GH. Compared with wild-type JAK2, which is constitutively active when overexpressed, JAK2 lacking tyrosine 868, 966, or 972 has substantially reduced activity. Coexpression with GH receptor and protein tyrosine phosphatase1B allowed us to investigate GH-dependent activation of these mutated JAK2s in human embryonic kidney 293T cells. All three mutated JAK2s are activated by GH, although to a lesser extent than wild-type JAK2. The three mutated JAK2s also mediate GH activation of signal transducer and activator of transcription 3 (Stat3), signal transducer and activator of transcription 5b (Stat5b) and ERK1, but at reduced levels. Coexpression with Src-homology 2B1beta (SH2B1beta), like coexpression with GH-bound GH receptor, partially restores the activity of all three JAK2 mutants. Based on these results and the crystal structure of the JAK2 kinase domain, we hypothesize that small changes in the conformation of the regions of JAK2 surrounding tyrosines 868, 966, and 972 due to e.g. phosphorylation, binding to a ligand-bound cytokine receptor, and/or binding to Src-homology 2B1, may be essential for JAK2 to assume a maximally active conformation.
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Affiliation(s)
- Lawrence S Argetsinger
- Department of Molecular and Integrative Physiology, The University of Michigan Medical School, Ann Arbor, Michigan 48109-5622, USA
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47
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Højlund K, Bowen BP, Hwang H, Flynn CR, Madireddy L, Geetha T, Langlais P, Meyer C, Mandarino LJ, Yi Z. In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS. J Proteome Res 2010; 8:4954-65. [PMID: 19764811 DOI: 10.1021/pr9007267] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein phosphorylation plays an essential role in signal transduction pathways that regulate substrate and energy metabolism, contractile function, and muscle mass in human skeletal muscle. Abnormal phosphorylation of signaling enzymes has been identified in insulin-resistant muscle using phosphoepitope-specific antibodies, but its role in other skeletal muscle disorders remains largely unknown. This may be in part due to insufficient knowledge of relevant targets. Here, we therefore present the first large-scale in vivo phosphoproteomic study of human skeletal muscle from 3 lean, healthy volunteers. Trypsin digestion of 3-5 mg human skeletal muscle protein was followed by phosphopeptide enrichment using SCX and TiO(2). The resulting phosphopeptides were analyzed by HPLC-ESI-MS/MS. Using this unbiased approach, we identified 306 distinct in vivo phosphorylation sites in 127 proteins, including 240 phosphoserines, 53 phosphothreonines, and 13 phosphotyrosines in at least 2 out of 3 subjects. In addition, 61 ambiguous phosphorylation sites were identified in at least 2 out of 3 subjects. The majority of phosphoproteins detected are involved in sarcomeric function, excitation-contraction coupling (the Ca(2+)-cycle), glycolysis, and glycogen metabolism. Of particular interest, we identified multiple novel phosphorylation sites on several sarcomeric Z-disk proteins known to be involved in signaling and muscle disorders. These results provide numerous new targets for the investigation of human skeletal muscle phosphoproteins in health and disease and demonstrate feasibility of phosphoproteomics research of human skeletal muscle in vivo.
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Affiliation(s)
- Kurt Højlund
- Center for Metabolic Biology, Arizona State University, Tempe, Arizona 85287-3704, USA
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48
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Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ. Phosphoproteomics for the masses. ACS Chem Biol 2010; 5:105-19. [PMID: 20047291 DOI: 10.1021/cb900277e] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation serves as a primary mechanism of signal transduction in the cells of biological organisms. Technical advancements over the last several years in mass spectrometry now allow for the large-scale identification and quantitation of in vivo phosphorylation at unprecedented levels. These developments have occurred in the areas of sample preparation, instrumentation, quantitative methodology, and informatics so that today, 10 000-20 000 phosphorylation sites can be identified and quantified within a few weeks. With the rapid development and widespread availability of such data, its translation into biological insight and knowledge is a current obstacle. Here we present an overview of how this technology came to be and is currently applied, as well as future challenges for the field.
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Affiliation(s)
| | | | | | - Nicole A. Beauchene
- Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Joshua J. Coon
- Departments of Chemistry
- Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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49
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Dunn JD, Reid GE, Bruening ML. Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. MASS SPECTROMETRY REVIEWS 2010; 29:29-54. [PMID: 19263479 DOI: 10.1002/mas.20219] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mass spectrometry is the tool of choice to investigate protein phosphorylation, which plays a vital role in cell regulation and diseases such as cancer. However, low abundances of phosphopeptides and low degrees of phosphorylation typically necessitate isolation and concentration of phosphopeptides prior to MS analysis. This review discusses the enrichment of phosphopeptides with immobilized metal affinity chromatography, reversible covalent binding, and metal oxide affinity chromatography. Capture of phosphopeptides on TiO(2) seems especially promising in terms of selectivity and recovery, but the success of all methods depends on careful selection of binding, washing, and elution solutions. Enrichment techniques are complementary, such that a combination of methods greatly enhances the number of phosphopeptides isolated from complex samples. Development of a standard series of phosphopeptides in a highly complex mixture of digested proteins would greatly aid the comparison of different enrichment methods. Phosphopeptide binding to magnetic beads and on-plate isolation prior to MALDI-MS are emerging as convenient methods for purification of small (microL) samples. On-plate enrichment can yield >70% recoveries of phosphopeptides in mixtures of a few digested proteins and can avoid sample-handling steps, but this technique is likely limited to relatively simple samples such as immunoprecipitates. With recent advances in enrichment techniques in hand, MS analysis should provide important insights into phosphorylation pathways.
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Affiliation(s)
- Jamie D Dunn
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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50
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Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, Ané JM, Coon JJ. Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. PLANT PHYSIOLOGY 2010; 152:19-28. [PMID: 19923235 PMCID: PMC2799343 DOI: 10.1104/pp.109.149625] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 11/11/2009] [Indexed: 05/20/2023]
Abstract
Nitrogen fixation in legumes requires the development of root organs called nodules and their infection by symbiotic rhizobia. Over the last decade, Medicago truncatula has emerged as a major model plant for the analysis of plant-microbe symbioses and for addressing questions pertaining to legume biology. While the initiation of symbiosis and the development of nitrogen-fixing root nodules depend on the activation of a protein phosphorylation-mediated signal transduction cascade in response to symbiotic signals produced by the rhizobia, few sites of in vivo phosphorylation have previously been identified in M. truncatula. We have characterized sites of phosphorylation on proteins from M. truncatula roots, from both whole cell lysates and membrane-enriched fractions, using immobilized metal affinity chromatography and tandem mass spectrometry. Here, we report 3,457 unique phosphopeptides spanning 3,404 nonredundant sites of in vivo phosphorylation on 829 proteins in M. truncatula Jemalong A17 roots, identified using the complementary tandem mass spectrometry fragmentation methods electron transfer dissociation and collision-activated dissociation. With this being, to our knowledge, the first large-scale plant phosphoproteomic study to utilize electron transfer dissociation, analysis of the identified phosphorylation sites revealed phosphorylation motifs not previously observed in plants. Furthermore, several of the phosphorylation motifs, including LxKxxs and RxxSxxxs, have yet to be reported as kinase specificities for in vivo substrates in any species, to our knowledge. Multiple sites of phosphorylation were identified on several key proteins involved in initiating rhizobial symbiosis, including SICKLE, NUCLEOPORIN133, and INTERACTING PROTEIN OF DMI3. Finally, we used these data to create an open-access online database for M. truncatula phosphoproteomic data.
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