1
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Callahan A, Chua XY, Griffith AA, Hildebrandt T, Fu G, Hu M, Wen R, Salomon AR. Deep phosphotyrosine characterisation of primary murine T cells using broad spectrum optimisation of selective triggering. Proteomics 2024:e2400106. [PMID: 39091061 DOI: 10.1002/pmic.202400106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
Sequencing the tyrosine phosphoproteome using MS-based proteomics is challenging due to the low abundance of tyrosine phosphorylation in cells, a challenge compounded in scarce samples like primary cells or clinical samples. The broad-spectrum optimisation of selective triggering (BOOST) method was recently developed to increase phosphotyrosine sequencing in low protein input samples by leveraging tandem mass tags (TMT), phosphotyrosine enrichment, and a phosphotyrosine-loaded carrier channel. Here, we demonstrate the viability of BOOST in T cell receptor (TCR)-stimulated primary murine T cells by benchmarking the accuracy and precision of the BOOST method and discerning significant alterations in the phosphoproteome associated with receptor stimulation. Using 1 mg of protein input (about 20 million cells) and BOOST, we identify and precisely quantify more than 2000 unique pY sites compared to about 300 unique pY sites in non-BOOST control samples. We show that although replicate variation increases when using the BOOST method, BOOST does not jeopardise quantitative precision or the ability to determine statistical significance for peptides measured in triplicate. Many pY previously uncharacterised sites on important T cell signalling proteins are quantified using BOOST, and we identify new TCR responsive pY sites observable only with BOOST. Finally, we determine that the phase-spectrum deconvolution method on Orbitrap instruments can impair pY quantitation in BOOST experiments.
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Affiliation(s)
- Aurora Callahan
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Xien Yu Chua
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Alijah A Griffith
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Tobias Hildebrandt
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
| | - Guoping Fu
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
| | - Mengzhou Hu
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
| | - Renren Wen
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
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2
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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. J Proteome Res 2023; 22:1868-1880. [PMID: 37097255 PMCID: PMC10510590 DOI: 10.1021/acs.jproteome.2c00850] [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] [Indexed: 04/26/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding the fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY can handle up to 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic, and tyrosine-specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
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Affiliation(s)
- Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
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3
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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522335. [PMID: 36711935 PMCID: PMC9881991 DOI: 10.1101/2023.01.05.522335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY handles 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic and tyrosine specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
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Affiliation(s)
- Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
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4
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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Kong Q, Ke M, Weng Y, Qin Y, He A, Li P, Cai Z, Tian R. Dynamic Phosphotyrosine-Dependent Signaling Profiling in Living Cells by Two-Dimensional Proximity Proteomics. J Proteome Res 2022; 21:2727-2735. [DOI: 10.1021/acs.jproteome.2c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qian Kong
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong 999077, Hong Kong SAR, China
| | - Mi Ke
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Yicheng Weng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Yunqiu Qin
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - An He
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Pengfei Li
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong 999077, Hong Kong SAR, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
- Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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6
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Kong Q, Weng Y, Zheng Z, Chen W, Li P, Cai Z, Tian R. Integrated and High-Throughput Approach for Sensitive Analysis of Tyrosine Phosphoproteome. Anal Chem 2022; 94:13728-13736. [PMID: 36179360 DOI: 10.1021/acs.analchem.2c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine phosphorylation (pTyr) regulates various signaling pathways under normal and cancerous states. Due to their low abundance and transient and dynamic natures, systematic profiling of pTyr sites is challenging. Antibody and engineered binding domain-based approaches have been well applied to pTyr peptide enrichment. However, traditional methods have the disadvantage of a long sample preparation process, which makes them unsuitable for processing limited amount of samples, especially in a high-throughput manner. In this study we developed a 96-well microplate-based approach to integrate all the sample preparation steps starting from cell culture to MS-compatible pTyr peptide enrichment in three consecutive 96-well microplates. By assembling an engineered SH2 domain onto a microplate, nonspecific adsorption of phosphopeptides is greatly reduced, which allows us to remove the Ti-IMAC purification and three C18 desalting steps (after digestion, pTyr enrichment, and Ti-IMAC purification) and, therefore, greatly simplifies the entire pTyr peptide enrichment workflow, especially when processing a large number of samples. Starting with 96-well microplate-cultured, pervanadate-stimulated cells, our approach could enrich 21% more pTyr sites than the traditional serial pTyr enrichment approach and showed good sensitivity and reproducibility in the range of 200 ng to 200 μg peptides. Importantly, we applied this approach to profile tyrosine kinase inhibitor-mediated EGFR signaling pathway and could well differentiate the distinct response of different pTyr sites. Collectively, the integrated 96-well microplate-based approach is valuable for profiling pTyr sites from limited biological samples and in a high-throughput manner.
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Affiliation(s)
- Qian Kong
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Yicheng Weng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zhendong Zheng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Wendong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Pengfei Li
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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7
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Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
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8
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Sanders KL, Edwards JL. Nano-liquid chromatography-mass spectrometry and recent applications in omics investigations. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4404-4417. [PMID: 32901622 PMCID: PMC7530103 DOI: 10.1039/d0ay01194k] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Liquid chromatography coupled to mass spectrometry (LC-MS) is one of the most powerful tools in identifying and quantitating molecular species. Decreasing column diameter from the millimeter to micrometer scale is now a well-developed method which allows for sample limited analysis. Specific fabrication of capillary columns is required for proper implementation and optimization when working in the nanoflow regime. Coupling the capillary column to the mass spectrometer for electrospray ionization (ESI) requires reduction of the subsequent emitter tip. Reduction of column diameter to capillary scale can produce improved chromatographic efficiency and the reduction of emitter tip size increased sensitivity of the electrospray process. This improved sensitivity and ionization efficiency is valuable in analysis of precious biological samples where analytes vary in size, ion affinity, and concentration. In this review we will discuss common approaches and challenges in implementing nLC-MS methods and how the advantages can be leveraged to investigate a wide range of biomolecules.
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9
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Chua XY, Mensah T, Aballo T, Mackintosh SG, Edmondson RD, Salomon AR. Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome. Mol Cell Proteomics 2020; 19:730-743. [PMID: 32071147 PMCID: PMC7124467 DOI: 10.1074/mcp.tir119.001865] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.
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Affiliation(s)
- Xien Yu Chua
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Theresa Mensah
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Timothy Aballo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
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10
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A polymer monolith composed of a perovskite and cucurbit[6]uril hybrid for highly selective enrichment of phosphopeptides prior to mass spectrometric analysis. Mikrochim Acta 2019; 187:68. [PMID: 31853651 DOI: 10.1007/s00604-019-4054-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022]
Abstract
A hybrid monolith was prepared from perovskite and cucurbit[6]uril [poly(hydroxyethyl methacrylate-pentaerythritol triacrylate) monolith] for the enrichment of phosphopeptides. By coupling with mass spectrometry, three goals were simultaneously realized, viz. (a) selective enrichment of phosphopeptides from non-phosphopeptides, (b) identification of mono- and multi-phosphopeptides, and (c) recognition of tyrosine phosphopeptides. The perovskite introduced into the monolith warrants high selectivity for phosphopeptides even at a high (10,000:1) ratio of non-phosphopeptides to phosphopeptides, and and enables identification of eight mono- and multi-phosphopeptides from standard β-casein tryptic digests. Tyrosine phosphopeptides were specifically detected via the recognition capability of cucurbit[6]uril integrated into the monolith. The method has remarkably specific enrichment capacity for phosphopeptides from samples including human serum, nonfat milk, and human acute myelocytic leukemia cell lysate. Graphical abstractSchematic representation of a monolith integrated with perovskite and cucurbit[6]uril. The monolithic column was coupled with mass spectrometry and applied to the enrichment of phosphopeptides. The method has remarkably specific enrichment capacity for phosphopeptides from complex biological samples.
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11
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Ma S, Li Y, Ma C, Wang Y, Ou J, Ye M. Challenges and Advances in the Fabrication of Monolithic Bioseparation Materials and their Applications in Proteomics Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902023. [PMID: 31502719 DOI: 10.1002/adma.201902023] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/29/2019] [Indexed: 06/10/2023]
Abstract
High-performance liquid chromatography integrated with tandem mass spectrometry (HPLC-MS/MS) has become a powerful technique for proteomics research. Its performance heavily depends on the separation efficiency of HPLC, which in turn depends on the chromatographic material. As the "heart" of the HPLC system, the chromatographic material is required to achieve excellent column efficiency and fast analysis. Monolithic materials, fabricated as continuous supports with interconnected skeletal structure and flow-through pores, are regarded as an alternative to particle-packed columns. Such materials are featured with easy preparation, fast mass transfer, high porosity, low back pressure, and miniaturization, and are next-generation separation materials for high-throughput proteins and peptides analysis. Herein, the recent progress regarding the fabrication of various monolithic materials is reviewed. Special emphasis is placed on studies of the fabrication of monolithic capillary columns and their applications in separation of biomolecules by capillary liquid chromatography (cLC). The applications of monolithic materials in the digestion, enrichment, and separation of phosphopeptides and glycopeptides from biological samples are also considered. Finally, advances in comprehensive 2D HPLC separations using monolithic columns are also shown.
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Affiliation(s)
- Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Ya Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Chen Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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12
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Pieroni L, Iavarone F, Olianas A, Greco V, Desiderio C, Martelli C, Manconi B, Sanna MT, Messana I, Castagnola M, Cabras T. Enrichments of post-translational modifications in proteomic studies. J Sep Sci 2019; 43:313-336. [PMID: 31631532 DOI: 10.1002/jssc.201900804] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
More than 300 different protein post-translational modifications are currently known, but only a few have been extensively investigated because modified proteoforms are commonly present in sub-stoichiometry amount. For this reason, improvement of specific enrichment techniques is particularly useful for the proteomic characterization of post-translationally modified proteins. Enrichment proteomic strategies could help the researcher in the challenging issue to decipher the complex molecular cross-talk existing between the different factors influencing the cellular pathways. In this review the state of art of the platforms applied for the enrichment of specific and most common post-translational modifications, such as glycosylation and glycation, phosphorylation, sulfation, redox modifications (i.e. sulfydration and nitrosylation), methylation, acetylation, and ubiquitinylation, are described. Enrichments strategies applied to characterize less studied post-translational modifications are also briefly discussed.
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Affiliation(s)
- Luisa Pieroni
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Federica Iavarone
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Viviana Greco
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudia Desiderio
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Irene Messana
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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13
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Yao Y, Wang Y, Wang S, Liu X, Liu Z, Li Y, Fang Z, Mao J, Zheng Y, Ye M. One-Step SH2 Superbinder-Based Approach for Sensitive Analysis of Tyrosine Phosphoproteome. J Proteome Res 2019; 18:1870-1879. [PMID: 30875230 DOI: 10.1021/acs.jproteome.9b00045] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tyrosine phosphorylation plays a major role in regulating cell signaling pathways governing diverse biological functions such as proliferation and differentiation. Systemically mapping phosphotyrosine (pTyr) sites is the key to understanding molecular mechanisms underlining pTyr-dependent signaling. Although mass spectrometry-based technologies have been widely used for pTyr site profiling and quantification, their applications are often hindered by the poor efficiency in current multistep enrichment procedures for inherently low abundance pTyr peptides, especially under physiological conditions. Taking advantage of the sequence-independent high affinity of SH2 superbinder toward pTyr residues, we have developed a simplified one-step pTyr peptide enrichment method that uses immobilized SH2 superbinder for unbiased and robust enrichment of endogenous pTyr peptides from biological samples. By eliminating the prerequisite global phosphopeptide enrichment step in our previously developed two-step method, we minimized sample loss and improved peptide capture efficiency. Applying this method to Jurkat cells at resting state, where the tyrosine phosphorylation level is low, both the number of identified pTyr peptides and sites are increased by three folds compared to the two-step method. Specifically, we were able to identify 511 nonredundant pTyr peptides, corresponding to 403 high confidence pTyr sites, from Jurkat cells with high level technical reproducibility (Pearson's correlation coefficient as high as 0.94). Further applying this method to two human breast cancer cell lines, BT474 and HCC1954, before and after EGF stimulation, we demonstrated that this approach could be a powerful tool for illustrating pTyr-dependent signaling network controlling cellular behaviors such as drug resistance.
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Affiliation(s)
- 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 (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yan 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 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Shujuan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Xiaoyan 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 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhen 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 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yanan Li
- 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 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zheng Fang
- 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 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , 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 (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yong Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , 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 (CAS) , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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