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Peng M, Zhou Y, Wan C. Identification of phosphorylated small ORF-encoded peptides in Hep3B cells by LC/MS/MS. J Proteomics 2024; 303:105214. [PMID: 38823442 DOI: 10.1016/j.jprot.2024.105214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Small ORF-encoded peptides (SEPs) are a class of low molecular weight proteins and peptides comprising <100 amino acids with important functions in various life activities. Although the sequence length is short, SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. In this work, we enriched phosphopeptides with IMAC and TiO2 materials and analyzed the phosphorylated SEPs in Hep3B cells. A total of 24 phosphorylated SEPs were identified, and 11 SEPs were coded by ncRNA. For the sequence analysis, we found that the general characteristics of phosphorylated SEPs are roughly the same as canonical proteins. Besides, two phosphorylation SEPs have the Stathmin family signature 2 motif, which can regulate the microtubule cytoskeleton. Some SEPs have domains or signal peptides, indicating their specific functions and subcellular locations. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of some SEPs. However, only one-fifth of the predicted phosphorylation sites were identified by LC/MS/MS, indicating that many SEP PTMs are hidden in the dark, waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation. SIGNIFICANCE: Small ORF-encoded peptides (SEPs) are important in various life activities. Although the sequence length is short (<100AA), SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. We enriched phosphopeptides and analyzed the phosphorylated SEPs in Hep3B cells. That is the first time to explore the PTM of SPEs systematically. Kinase network analysis found a small number of kinases that may be a clue to the specific functions of SEPs. More SEP PTMs are hidden in the dark and waiting to be uncovered and verified. This study helps expand our understanding of SEP and provides information for further SEP function investigation.
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Affiliation(s)
- Mingbo Peng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yutian Zhou
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.
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2
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Wang Y, Li R, Shu W, Chen X, Lin Y, Wan J. Designed Nanomaterials-Assisted Proteomics and Metabolomics Analysis for In Vitro Diagnosis. SMALL METHODS 2024; 8:e2301192. [PMID: 37922520 DOI: 10.1002/smtd.202301192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/12/2023] [Indexed: 11/05/2023]
Abstract
In vitro diagnosis (IVD) is pivotal in modern medicine, enabling early disease detection and treatment optimization. Omics technologies, particularly proteomics and metabolomics, offer profound insights into IVD. Despite its significance, omics analyses for IVD face challenges, including low analyte concentrations and the complexity of biological environments. In addition, the direct omics analysis by mass spectrometry (MS) is often hampered by issues like large sample volume requirements and poor ionization efficiency. Through manipulating their size, surface charge, and functionalization, as well as the nanoparticle-fluid incubation conditions, nanomaterials have emerged as a promising solution to extract biomolecules and enhance the desorption/ionization efficiency in MS detection. This review delves into the last five years of nanomaterial applications in omics, focusing on their role in the enrichment, separation, and ionization analysis of proteins and metabolites for IVD. It aims to provide a comprehensive update on nanomaterial design and application in omics, highlighting their potential to revolutionize IVD.
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Affiliation(s)
- Yanhui Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Rongxin Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Weikang Shu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Xiaonan Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Yingying Lin
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
| | - Jingjing Wan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China
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3
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Duan X, Zhang Y, Huang X, Ma X, Gao H, Wang Y, Xiao Z, Huang C, Wang Z, Li B, Yang W, Wang Y. GreenPhos, a universal method for in-depth measurement of plant phosphoproteomes with high quantitative reproducibility. MOLECULAR PLANT 2024; 17:199-213. [PMID: 38018035 DOI: 10.1016/j.molp.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
Protein phosphorylation regulates a variety of important cellular and physiological processes in plants. In-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal phosphoproteomes. This is largely due to the need to improve protein extraction efficiency from plant cells, which have a dense cell wall, and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry analysis. To this end, we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis, rice, tomato, and Chlamydomonas reinhardtii, enabling in-depth identification with high quantitative reproducibility of about 11 000 phosphosites, the greatest depth achieved so far with single liquid chromatography-mass spectrometry (LC-MS) runs operated in a data-dependent acquisition (DDA) mode. The mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time- and cost-effectiveness. The method, named GreenPhos, combined with single-shot LC-MS, enabled in-depth quantitative identification of Arabidopsis phosphoproteins, including differentially phosphorylated spliceosomal proteins, at multiple time points during salt stress and a number of kinase substrate motifs. GreenPhos is expected to serve as a universal method for purification of plant phosphopeptides, which, if samples are further fractionated and analyzed by multiple LC-MS runs, could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.
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Affiliation(s)
- Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongshu Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bolong Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Koch JP, Roth SM, Quintin A, Gavini J, Orlando E, Riedo R, Pozzato C, Hayrapetyan L, Aebersold R, Stroka DM, Aebersold DM, Medo M, Zimmer Y, Medová M. A DNA-PK phosphorylation site on MET regulates its signaling interface with the DNA damage response. Oncogene 2023; 42:2113-2125. [PMID: 37188738 PMCID: PMC10289896 DOI: 10.1038/s41388-023-02714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
The DNA damage response (DDR) is intertwined with signaling pathways downstream of oncogenic receptor tyrosine kinases (RTKs). To drive research into the application of targeted therapies as radiosensitizers, a better understanding of this molecular crosstalk is necessary. We present here the characterization of a previously unreported MET RTK phosphosite, Serine 1016 (S1016) that represents a potential DDR-MET interface. MET S1016 phosphorylation increases in response to irradiation and is mainly targeted by DNA-dependent protein kinase (DNA-PK). Phosphoproteomics unveils an impact of the S1016A substitution on the overall long-term cell cycle regulation following DNA damage. Accordingly, the abrogation of this phosphosite strongly perturbs the phosphorylation of proteins involved in the cell cycle and formation of the mitotic spindle, enabling cells to bypass a G2 arrest upon irradiation and leading to the entry into mitosis despite compromised genome integrity. This results in the formation of abnormal mitotic spindles and a lower proliferation rate. Altogether, the current data uncover a novel signaling mechanism through which the DDR uses a growth factor receptor system for regulating and maintaining genome stability.
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Affiliation(s)
- Jonas P Koch
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Selina M Roth
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Aurélie Quintin
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Jacopo Gavini
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
| | - Eleonora Orlando
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Rahel Riedo
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Chiara Pozzato
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Liana Hayrapetyan
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3010, Bern, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
- Faculty of Science, University of Zürich, 8057, Zürich, Switzerland
| | - Deborah M Stroka
- Department for BioMedical Research, Visceral Surgery, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
| | - Daniel M Aebersold
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Matúš Medo
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Yitzhak Zimmer
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland
| | - Michaela Medová
- Department for BioMedical Research, Radiation Oncology, Inselspital, Bern University Hospital, and University of Bern, Bern, Switzerland.
- Department of Radiation Oncology, Inselspital, Bern University Hospital, Freiburgstrasse 8, 3008, Bern, Switzerland.
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5
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Brown NW, Schlomach SK, Marmelstein AM, Fiedler D. Chemoselective Labeling and Immobilization of Phosphopeptides with Phosphorimidazolide Reagents. Chembiochem 2023; 24:e202200407. [PMID: 36166450 DOI: 10.1002/cbic.202200407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/21/2022] [Indexed: 11/11/2022]
Abstract
Protein phosphorylation is one of the most ubiquitous post-translational modifications, regulating numerous essential processes in cells. Accordingly, the large-scale annotation of phosphorylation sites continues to provide central insight into the regulation of signaling networks. The global analysis of the phosphoproteome typically relies on mass spectrometry analysis of phosphopeptides, with an enrichment step necessary due to the sub-stoichiometric nature of phosphorylation. Several affinity-based methods and chemical modification strategies have been developed to date, but the choice of enrichment method can have a considerable impact on the results. Here, we show that a biotinylated, photo-cleavable phosphorimidazolide reagent permits the immobilization and subsequent cleavage of phosphopeptides. The method is capable of the capture and release of phosphopeptides of varying characteristics, and this mild and selective strategy expands the current repertoire for phosphopeptide chemical modification with the potential to enrich and identify new phosphorylation sites in the future.
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Affiliation(s)
- Nathaniel W Brown
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Princeton University, Washington Rd., Princeton, NJ 08544, USA
| | - Sandra K Schlomach
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Alan M Marmelstein
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Princeton University, Washington Rd., Princeton, NJ 08544, USA
| | - Dorothea Fiedler
- Department of Chemical Biology, Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.,Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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6
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Poudel S, Vanderwall D, Yuan ZF, Wu Z, Peng J, Li Y. JUMPptm: Integrated software for sensitive identification of post-translational modifications and its application in Alzheimer's disease study. Proteomics 2023; 23:e2100369. [PMID: 36094355 PMCID: PMC9957936 DOI: 10.1002/pmic.202100369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment of modified proteins or peptides. However, recent ultra-deep whole proteome profiling generates millions of spectra in a single experiment, leaving many unassigned spectra, some of which may be derived from PTM peptides. METHODS Here we present JUMPptm, an integrative computational pipeline, to extract PTMs from unenriched whole proteome. JUMPptm combines the advantages of JUMP, MSFragger and Comet search engines, and includes de novo tags, customized database search and peptide filtering, which iteratively analyzes each PTM by a multi-stage strategy to improve sensitivity and specificity. RESULTS We applied JUMPptm to the deep brain proteome of Alzheimer's disease (AD), and identified 34,954 unique peptides with phosphorylation, methylation, acetylation, ubiquitination, and others. The phosphorylated peptides were validated by enriched phosphoproteome from the same sample. TMT-based quantification revealed 482 PTM peptides dysregulated at different stages during AD progression. For example, the acetylation of numerous mitochondrial proteins is significantly decreased in AD. A total of 60 PTM sites are found in the pan-PTM map of the Tau protein. CONCLUSION The JUMPptm program is an effective tool for pan-PTM analysis and the resulting AD pan-PTM profile serves as a valuable resource for AD research.
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Affiliation(s)
- Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David Vanderwall
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Correspondence: and
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Correspondence: and
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7
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Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
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8
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An oncogene addiction phosphorylation signature and its derived scores inform tumor responsiveness to targeted therapies. Cell Mol Life Sci 2022; 80:6. [PMID: 36494469 PMCID: PMC9734221 DOI: 10.1007/s00018-022-04634-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE Oncogene addiction provides important therapeutic opportunities for precision oncology treatment strategies. To date the cellular circuitries associated with driving oncoproteins, which eventually establish the phenotypic manifestation of oncogene addiction, remain largely unexplored. Data suggest the DNA damage response (DDR) as a central signaling network that intersects with pathways associated with deregulated addicting oncoproteins with kinase activity in cancer cells. EXPERIMENTAL DESIGN: We employed a targeted mass spectrometry approach to systematically explore alterations in 116 phosphosites related to oncogene signaling and its intersection with the DDR following inhibition of the addicting oncogene alone or in combination with irradiation in MET-, EGFR-, ALK- or BRAF (V600)-positive cancer models. An NSCLC tissue pipeline combining patient-derived xenografts (PDXs) and ex vivo patient organotypic cultures has been established for treatment responsiveness assessment. RESULTS We identified an 'oncogene addiction phosphorylation signature' (OAPS) consisting of 8 protein phosphorylations (ACLY S455, IF4B S422, IF4G1 S1231, LIMA1 S490, MYCN S62, NCBP1 S22, P3C2A S259 and TERF2 S365) that are significantly suppressed upon targeted oncogene inhibition solely in addicted cell line models and patient tissues. We show that the OAPS is present in patient tissues and the OAPS-derived score strongly correlates with the ex vivo responses to targeted treatments. CONCLUSIONS We propose a score derived from OAPS as a quantitative measure to evaluate oncogene addiction of cancer cell samples. This work underlines the importance of protein phosphorylation assessment for patient stratification in precision oncology and corresponding identification of tumor subtypes sensitive to inhibition of a particular oncogene.
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Zhang N, Huang T, Xie P, Yang Z, Zhang L, Wu X, Cai Z. Epitaxial Growth of Guanidyl-Functionalized Magnetic Metal-Organic Frameworks with Multiaffinity Sites for Selective Capture of Global Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2022; 14:39364-39374. [PMID: 35993677 DOI: 10.1021/acsami.2c10353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The flexible and controlled synthesis of metal-organic framework (MOF)-derived hybrid nanostructures is of great significance in fine tuning of their enrichment performance in large-scale and in-depth phosphoproteome analysis. Herein, a magnetic guanidyl-functionalized MOF hybrid coating with multiaffinity sites, denoted as Fe3O4@G-ZIF-8, was fast fabricated via a one-pot epitaxial growth strategy for the first time and applied for selective and highly efficient enrichment of global phosphopeptides. The intrinsic unsaturated metal sites of ZIF-8 endow the surface-mounted MOF coatings with immobilized metal ion affinity chromatography interaction with multiphosphorylated peptides. The oriented anchoring of bifunctional guanidineacetic acid on the magnetic MOF nanospheres provides additional affinity sites (guanidyl groups) for specific recognition of phosphopeptides by "salt bridge" interaction, as well as active site carboxyl groups for the coordination with the metal ions. The as-prepared Fe3O4@G-ZIF-8 exhibits large surface area (382.5 m2 g-1), good superparamagnetic property (41.6 emu g-1) and stability, and size-exclusion effect (1.73 nm), which can serve as a specific adsorbent for global phosphopeptide analysis with satisfactory selectivity, great detection sensitivity (1 fmol), and rapid magnetic separation. Moreover, the successful application of Fe3O4@G-ZIF-8 for selective capture of both multi- and mono-phosphopeptides from human saliva and serum demonstrated the great potential of magnetic surface-mounted MOF coatings in effective identification of low-abundance phosphopeptides by matrix-assisted laser desorption ionization time-of-flight mass spectrometry from complicated biological matrices.
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Affiliation(s)
- Ning Zhang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
- Institute of Environmental and Analytical Science, School of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, Henan, P. R. China
| | - Ting Huang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Peisi Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, SAR, China
| | - Zhu Yang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, SAR, China
| | - Lan Zhang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xiaoping Wu
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology; College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, SAR, China
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10
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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11
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Wan N, Wang N, Yu S, Zhang H, Tang S, Wang D, Lu W, Li H, Delafield DG, Kong Y, Wang X, Shao C, Lv L, Wang G, Tan R, Wang N, Hao H, Ye H. Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome. Nat Methods 2022; 19:854-864. [PMID: 35761067 DOI: 10.1038/s41592-022-01523-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 05/13/2022] [Indexed: 12/18/2022]
Abstract
Lactylation was initially discovered on human histones. Given its nascence, its occurrence on nonhistone proteins and downstream functional consequences remain elusive. Here we report a cyclic immonium ion of lactyllysine formed during tandem mass spectrometry that enables confident protein lactylation assignment. We validated the sensitivity and specificity of this ion for lactylation through affinity-enriched lactylproteome analysis and large-scale informatic assessment of nonlactylated spectral libraries. With this diagnostic ion-based strategy, we confidently determined new lactylation, unveiling a wide landscape beyond histones from not only the enriched lactylproteome but also existing unenriched human proteome resources. Specifically, by mining the public human Meltome Atlas, we found that lactylation is common on glycolytic enzymes and conserved on ALDOA. We also discovered prevalent lactylation on DHRS7 in the draft of the human tissue proteome. We partially demonstrated the functional importance of lactylation: site-specific engineering of lactylation into ALDOA caused enzyme inhibition, suggesting a lactylation-dependent feedback loop in glycolysis.
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Affiliation(s)
- Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Nian Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Siqin Yu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hanqing Zhang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Shuo Tang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Dexiang Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Wenjie Lu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Huanhuan Li
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Daniel G Delafield
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Kong
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xinmiao Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Langlang Lv
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Guangji Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Renxiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Nanxi Wang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China. .,School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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12
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Comprehensive Evaluation of Different TiO2-Based Phosphopeptide Enrichment and Fractionation Methods for Phosphoproteomics. Cells 2022; 11:cells11132047. [PMID: 35805136 PMCID: PMC9265536 DOI: 10.3390/cells11132047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Protein phosphorylation is an essential post-translational modification that regulates multiple cellular processes. Due to their low stoichiometry and ionization efficiency, it is critical to efficiently enrich phosphopeptides for phosphoproteomics. Several phosphopeptide enrichment methods have been reported; however, few studies have comprehensively compared different TiO2-based phosphopeptide enrichment methods using complex proteomic samples. Here, we compared four TiO2-based phosphopeptide enrichment methods that used four non-phosphopeptide excluders (glutamic acid, lactic acid, glycolic acid, and DHB). We found that these four TiO2-based phosphopeptide enrichment methods had different enrichment specificities and that phosphopeptides enriched by the four methods had different physicochemical characteristics. More importantly, we discovered that phosphopeptides had a higher deamidation ratio than peptides from cell lysate and that phosphopeptides enriched using the glutamic acid method had a higher deamidation ratio than the other three methods. We then compared two phosphopeptide fractionation methods: ammonia- or TEA-based high pH reversed-phase (HpH-RP). We found that fewer phosphopeptides, especially multi-phosphorylated peptides, were identified using the ammonia-based method than using the TEA-based method. Therefore, the TEA-based HpH-RP fractionation method performed better than the ammonia method. In conclusion, we comprehensively evaluated different TiO2-based phosphopeptide enrichment and fractionation methods, providing a basis for selecting the proper protocols for comprehensive phosphoproteomics.
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13
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Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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14
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Carregari VC. Phosphopeptide Enrichment Techniques: A Pivotal Step for Phosphoproteomic Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:17-27. [DOI: 10.1007/978-3-031-05460-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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15
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Sanford EJ, Smolka MB. Fe-NTA Microcolumn Purification of Phosphopeptides from Immunoprecipitation (IP) Eluates for Mass Spectrometry Analysis. Bio Protoc 2021; 11:e4113. [PMID: 34458407 DOI: 10.21769/bioprotoc.4113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/18/2021] [Accepted: 04/30/2021] [Indexed: 11/02/2022] Open
Abstract
Protein phosphorylation is a nearly universal signaling mechanism. To date, a number of proteomics tools have been developed to analyze phosphorylation. Phosphoproteome-wide analyses using whole cell extracts suffer from incomplete coverage, often missing phosphorylation events from low-abundance proteins. In order to increase coverage of phosphorylation sites on individual proteins of interest ("phospho-mapping"), immunoprecipitation (IP) followed by phosphoenrichment is necessary. Unfortunately, most commercially available phosphoenrichment kits are not readily scalable to the low-microgram quantities of protein present in IP eluates. Here, we describe a simple method specifically optimized for the enrichment of phosphopeptides from IP samples using an Fe-NTA based method. This method can be added downstream of any standard immunoprecipitation protocol and upstream of any MS analysis pipeline. The protocol described herein is cost effective, uses commonly available laboratory reagents, and can be used to obtain deep coverage of individual protein phosphorylation patterns, supplementary to phosphoproteomics data. Graphical abstract: Phospho-mapping workflow for a hypothetical protein of interest.
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Affiliation(s)
- Ethan J Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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16
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Gerritsen JS, White FM. Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells. Expert Rev Proteomics 2021; 18:661-674. [PMID: 34468274 PMCID: PMC8628306 DOI: 10.1080/14789450.2021.1976152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Many pathologies, including cancer, have been associated with aberrant phosphorylation-mediated signaling networks that drive altered cell proliferation, migration, metabolic regulation, and can lead to systemic inflammation. Phosphoproteomics, the large-scale analysis of protein phosphorylation sites, has emerged as a powerful tool to define signaling network regulation and dysregulation in normal and pathological conditions. AREAS COVERED We provide an overview of methodology for global phosphoproteomics as well as enrichment of specific subsets of the phosphoproteome, including phosphotyrosine and phospho-motif enrichment of kinase substrates. We review quantitative methods, advantages and limitations of different mass spectrometry acquisition formats, and computational approaches to extract biological insight from phosphoproteomics data. Throughout, we discuss various applications and their challenges in implementation. EXPERT OPINION Over the past 20 years the field of phosphoproteomics has advanced to enable deep biological and clinical insight through the quantitative analysis of signaling networks. Future areas of development include Clinical Laboratory Improvement Amendments (CLIA)-approved methods for analysis of clinical samples, continued improvements in sensitivity to enable analysis of small numbers of rare cells and tissue microarrays, and computational methods to integrate data resulting from multiple systems-level quantitative analytical methods.
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Affiliation(s)
- Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
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17
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Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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18
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Dunphy K, Dowling P, Bazou D, O’Gorman P. Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers. Cancers (Basel) 2021; 13:1930. [PMID: 33923680 PMCID: PMC8072572 DOI: 10.3390/cancers13081930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
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19
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Borne AL, Brulet JW, Yuan K, Hsu KL. Development and biological applications of sulfur-triazole exchange (SuTEx) chemistry. RSC Chem Biol 2021; 2:322-337. [PMID: 34095850 PMCID: PMC8174820 DOI: 10.1039/d0cb00180e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/27/2022] Open
Abstract
Sulfur electrophiles constitute an important class of covalent small molecules that have found widespread applications in synthetic chemistry and chemical biology. Various electrophilic scaffolds, including sulfonyl fluorides and arylfluorosulfates as recent examples, have been applied for protein bioconjugation to probe ligand sites amenable for chemical proteomics and drug discovery. In this review, we describe the development of sulfonyl-triazoles as a new class of electrophiles for sulfur-triazole exchange (SuTEx) chemistry. SuTEx achieves covalent reaction with protein sites through irreversible modification of a residue with an adduct group (AG) upon departure of a leaving group (LG). A principal differentiator of SuTEx from other chemotypes is the selection of a triazole heterocycle as the LG, which introduces additional capabilities for tuning the sulfur electrophile. We describe the opportunities afforded by modifications to the LG and AG alone or in tandem to facilitate nucleophilic substitution reactions at the SO2 center in cell lysates and live cells. As a result of these features, SuTEx serves as an efficient platform for developing chemical probes with tunable bioactivity to study novel nucleophilic sites on established and poorly annotated protein targets. Here, we highlight a suite of biological applications for the SuTEx electrophile and discuss future goals for this enabling covalent chemistry.
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Affiliation(s)
- Adam L. Borne
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
| | - Jeffrey W. Brulet
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Kun Yuan
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
- University of Virginia Cancer Center, University of VirginiaCharlottesvilleVA 22903USA
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleVirginia 22908USA
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20
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Comprehensive Protocol to Simultaneously Study Protein Phosphorylation, Acetylation, and N-Linked Sialylated Glycosylation. Methods Mol Biol 2021. [PMID: 33420984 DOI: 10.1007/978-1-0716-1186-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
Posttranslational modifications (PTMs) such as phosphorylation, acetylation, and glycosylation are an essential regulatory mechanism of protein function and interaction, and they are associated with a wide range of biological processes. Since most PTMs alter the molecular mass of a protein, mass spectrometry (MS) is the ideal analytical tool for studying various PTMs. However, PTMs are often present in substoichiometric levels, and therefore their unmodified counterpart often suppresses their signal in MS. Consequently, PTM analysis by MS is a challenging task, requiring highly specialized and sensitive PTM-specific enrichment methods. Currently, several methods have been implemented for PTM enrichment, and each of them has its drawbacks and advantages as they differ in selectivity and specificity toward specific protein modifications. Unfortunately, for the vast majority of more than 400 known modifications, we have no or poor tools for selective enrichment.Here, we describe a comprehensive workflow to simultaneously study phosphorylation, acetylation, and N-linked sialylated glycosylation from the same biological sample. The protocol involves an initial titanium dioxide (TiO2) step to enrich for phosphopeptides and sialylated N-linked glycopeptides followed by glycan release and post-fractionation using sequential elution from immobilized metal affinity chromatography (SIMAC) to separate mono-phosphorylated and deglycosylated peptides from multi-phosphorylated ones. The IMAC flow-through and acidic elution are subsequently subjected to a next round of TiO2 enrichment for further separation of mono-phosphopeptides from deglycosylated peptides. Furthermore, the lysine-acetylated peptides present in the first TiO2 flow-through fraction are enriched by immunoprecipitation (IP) after peptide cleanup. Finally, the samples are fractionated by high pH reversed phase chromatography (HpH) or hydrophilic interaction liquid chromatography (HILIC ) to reduce sample complexity and increase the coverage in the subsequent LC-MS /MS analysis. This allows the analysis of multiple types of modifications from the same highly complex biological sample without decreasing the quality of each individual PTM study.
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21
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Label-Free Quantitative Phosphoproteomics of the Fission Yeast Schizosaccharomyces pombe Using Strong Anion Exchange- and Porous Graphitic Carbon-Based Fractionation Strategies. Int J Mol Sci 2021; 22:ijms22041747. [PMID: 33572424 PMCID: PMC7916215 DOI: 10.3390/ijms22041747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/26/2022] Open
Abstract
The phosphorylation of proteins modulates various functions of proteins and plays an important role in the regulation of cell signaling. In recent years, label-free quantitative (LFQ) phosphoproteomics has become a powerful tool to analyze the phosphorylation of proteins within complex samples. Despite the great progress, the studies of protein phosphorylation are still limited in throughput, robustness, and reproducibility, hampering analyses that involve multiple perturbations, such as those needed to follow the dynamics of phosphoproteomes. To address these challenges, we introduce here the LFQ phosphoproteomics workflow that is based on Fe-IMAC phosphopeptide enrichment followed by strong anion exchange (SAX) and porous graphitic carbon (PGC) fractionation strategies. We applied this workflow to analyze the whole-cell phosphoproteome of the fission yeast Schizosaccharomyces pombe. Using this strategy, we identified 8353 phosphosites from which 1274 were newly identified. This provides a significant addition to the S. pombe phosphoproteome. The results of our study highlight that combining of PGC and SAX fractionation strategies substantially increases the robustness and specificity of LFQ phosphoproteomics. Overall, the presented LFQ phosphoproteomics workflow opens the door for studies that would get better insight into the complexity of the protein kinase functions of the fission yeast S. pombe.
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22
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Lanz MC, Yugandhar K, Gupta S, Sanford EJ, Faça VM, Vega S, Joiner AMN, Fromme JC, Yu H, Smolka MB. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep 2021; 22:e51121. [PMID: 33491328 PMCID: PMC7857435 DOI: 10.15252/embr.202051121] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 01/11/2023] Open
Abstract
Phosphorylation is one of the most dynamic and widespread post-translational modifications regulating virtually every aspect of eukaryotic cell biology. Here, we assemble a dataset from 75 independent phosphoproteomic experiments performed in our laboratory using Saccharomyces cerevisiae. We report 30,902 phosphosites identified from cells cultured in a range of DNA damage conditions and/or arrested in distinct cell cycle stages. To generate a comprehensive resource for the budding yeast community, we aggregate our dataset with the Saccharomyces Genome Database and another recently published study, resulting in over 46,000 budding yeast phosphosites. With the goal of enhancing the identification of functional phosphorylation events, we perform computational positioning of phosphorylation sites on available 3D protein structures and systematically identify events predicted to regulate protein complex architecture. Results reveal hundreds of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic "clashes" predicted to disrupt the interaction. With the advancement of Cryo-EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.
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Affiliation(s)
- Michael C Lanz
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
- Present address:
Department of BiologyStanford UniversityStanfordCAUSA
| | - Kumar Yugandhar
- Department of Computational BiologyWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Shagun Gupta
- Department of Computational BiologyWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Ethan J Sanford
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Vitor M Faça
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Stephanie Vega
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Aaron M N Joiner
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - J Christopher Fromme
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Haiyuan Yu
- Department of Computational BiologyWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus B Smolka
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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23
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Genome-Wide Proteomics and Phosphoproteomics Analysis of Trypanosoma cruzi During Differentiation. Methods Mol Biol 2021; 2116:139-159. [PMID: 32221920 DOI: 10.1007/978-1-0716-0294-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Trypanosoma cruzi is a pathogenic protozoan that still has an impact on public health, despite the decrease in the number of infection cases along the years. T. cruzi possesses an heteroxenic life cycle in which it differentiates in at least four forms. Among the differentiation processes, metacyclogenesis has been exploited in different views by researchers. An intriguing question that rises is how metacyclogenesis is triggered and controlled by cell signaling and which are the differentially expressed proteins and posttranslational modifications involved in this process. An important cell signaling pathway is the protein phosphorylation, and it is reinforced in T. cruzi in which the gene expression control occurs almost exclusively posttranscriptionally. Additionally, the number of protein kinases in T. cruzi is relatively high compared to other organisms. A way to approach these questions is evaluating the cells through phosphoproteomics and proteomics. In this chapter, we will describe the steps from the cell protein extraction, digestion and fractionation, phosphopeptide enrichment, to LC-MS/MS analysis as well as a brief overview on peptide identification. In addition, a published method for in vitro metacyclogenesis will be detailed.
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24
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25
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Huang X, Zhang Y, Ge H, Lu D, Wang Y. Plant Phosphopeptides Enrichment by Immobilized Metal Ion Affinity Chromatography. Methods Mol Biol 2021; 2358:145-157. [PMID: 34270052 DOI: 10.1007/978-1-0716-1625-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation plays important roles in the regulation of plant growth and development as well as adaption to changing environments. Large-scale identification of the phosphorylated proteins could provide both a global view of and specific targets involved in the mechanism underlying these processes. The progress of phosphoproteomic study for higher plants has lagged behind that of animals due to technical challenges, particularly the difficulty in solubilizing proteins from plant tissues with a rigid cell wall and the interference of the secondary metabolites, polysaccharides, and pigments throughout the whole processes of sample preparation and LC-MS analysis. Thus, it is critical to improve the efficiency of protein extraction and to remove the interfering metabolites before phosphopeptides enrichment. Here we describe a protocol for plant protein extraction and phosphopeptides enrichment by Fe3+-immobilized metal ion affinity chromatography (Fe3+-IMAC). Strong detergents such as SDS were used to extract proteins from plant tissues, and the secondary metabolites were removed by protein precipitation and washing of the pellets. The protein samples were digested and the resulting peptides were prefractionated. Phosphopeptides enriched from each fraction were combined before analysis with LC-MS.
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Affiliation(s)
- Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovation Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, The Innovation Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, The Innovation Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovation Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
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He M, Li Z. The Application of an R Language-Based Platform cRacker for Phosphoproteomics Data Analysis. Methods Mol Biol 2021; 2358:221-228. [PMID: 34270058 DOI: 10.1007/978-1-0716-1625-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Phosphoproteomics has drawn great attention of biologist since phosphorylation is proven to play an important role in regulation of proteins. Mass spectrometry technology has helped with the development of phosphoproteomics due to its ability in generating large amount of detailed information after analyzing the phosphoproteome samples. However, interpreting the phosphoproteome data deprived from mass spectrometry can be time-consuming. Here, we introduced a free R language-based platform which can be used in accelerating phosphoproteome data analysis. This platform has integrated different functions and methods which are popularly used in phosphoproteome data analysis, so users can customize their analysis according to their demands.
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Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
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Finamore F, Ucciferri N, Signore G, Cecchettini A, Ceccherini E, Vitiello M, Poliseno L, Rocchiccioli S. Proteomics pipeline for phosphoenrichment and its application on a human melanoma cell model. Talanta 2020; 220:121381. [PMID: 32928406 DOI: 10.1016/j.talanta.2020.121381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 11/25/2022]
Abstract
Cell signalling is tightly regulated by post-translational modification of proteins. Among them, phosphorylation is one of the most interesting and important. Identifying phosphorylation sites on proteins is challenging and requires strategies for pre-separation and enrichment of the phosphorylated species. We applied four different methods for phospho-enrichment involving TiO2 and IMAC matrix to human melanoma cell lysates of starved A375 induced for 1 h with 1% FBS. Comparison of protocol efficiency was evaluated through peptide concentration, sulphur and phosphorus content and peptide analysis by LC-MS in the collected fractions. Our results underlined that each single method is not sufficient for a comprehensive phosphoproteome analysis. In fact, each methodology permits to identify only a fraction of the phosphoproteome contained in a whole cell lysate. The selection of the most efficient protocols and a combination of two phospho-enrichment methods allowed the assessment of this workflow able to pinpoint the main actors in the phospho-proteome cascade of A375 human melanoma cells treated with Vemurafenib.
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Affiliation(s)
- Francesco Finamore
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy
| | - Nadia Ucciferri
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy
| | - Giovanni Signore
- NEST, Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, 56127, Italy; Fondazione Pisana per la Scienza ONLUS, via Ferruccio Giovannini 13, San Giuliano Terme, 56017, Italy
| | - Antonella Cecchettini
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy; Dept of Clinical and Experimental Medicine, Pisa University, via Volta 4, 56126, Pisa, Italy
| | - Elisa Ceccherini
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy
| | - Marianna Vitiello
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy; Oncogenomics Unit, ISPRO, via Moruzzi 1, Pisa, 56124, Italy
| | - Laura Poliseno
- Institute of Clinical Physiology, CNR, via Moruzzi 1, Pisa, 56124, Italy; Oncogenomics Unit, ISPRO, via Moruzzi 1, Pisa, 56124, Italy
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Schlam-Babayov S, Bensimon A, Harel M, Geiger T, Aebersold R, Ziv Y, Shiloh Y. Phosphoproteomics reveals novel modes of function and inter-relationships among PIKKs in response to genotoxic stress. EMBO J 2020; 40:e104400. [PMID: 33215756 DOI: 10.15252/embj.2020104400] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023] Open
Abstract
The DNA damage response (DDR) is a complex signaling network that relies on cascades of protein phosphorylation, which are initiated by three protein kinases of the family of PI3-kinase-related protein kinases (PIKKs): ATM, ATR, and DNA-PK. ATM is missing or inactivated in the genome instability syndrome, ataxia-telangiectasia (A-T). The relative shares of these PIKKs in the response to genotoxic stress and the functional relationships among them are central questions in the genome stability field. We conducted a comprehensive phosphoproteomic analysis in human wild-type and A-T cells treated with the double-strand break-inducing chemical, neocarzinostatin, and validated the results with the targeted proteomic technique, selected reaction monitoring. We also matched our results with 34 published screens for DDR factors, creating a valuable resource for identifying strong candidates for novel DDR players. We uncovered fine-tuned dynamics between the PIKKs following genotoxic stress, such as DNA-PK-dependent attenuation of ATM. In A-T cells, partial compensation for ATM absence was provided by ATR and DNA-PK, with distinct roles and kinetics. The results highlight intricate relationships between these PIKKs in the DDR.
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Affiliation(s)
- Sapir Schlam-Babayov
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Michal Harel
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Yael Ziv
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Yosef Shiloh
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
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Thingholm TE, Rönnstrand L, Rosenberg PA. Why and how to investigate the role of protein phosphorylation in ZIP and ZnT zinc transporter activity and regulation. Cell Mol Life Sci 2020; 77:3085-3102. [PMID: 32076742 PMCID: PMC7391401 DOI: 10.1007/s00018-020-03473-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/13/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Zinc is required for the regulation of proliferation, metabolism, and cell signaling. It is an intracellular second messenger, and the cellular level of ionic, mobile zinc is strictly controlled by zinc transporters. In mammals, zinc homeostasis is primarily regulated by ZIP and ZnT zinc transporters. The importance of these transporters is underscored by the list of diseases resulting from changes in transporter expression and activity. However, despite numerous structural studies of the transporters revealing both zinc binding sites and motifs important for transporter function, the exact molecular mechanisms regulating ZIP and ZnT activities are still not clear. For example, protein phosphorylation was found to regulate ZIP7 activity resulting in the release of Zn2+ from intracellular stores leading to phosphorylation of tyrosine kinases and activation of signaling pathways. In addition, sequence analyses predict all 24 human zinc transporters to be phosphorylated suggesting that protein phosphorylation is important for regulation of transporter function. This review describes how zinc transporters are implicated in a number of important human diseases. It summarizes the current knowledge regarding ZIP and ZnT transporter structures and points to how protein phosphorylation seems to be important for the regulation of zinc transporter activity. The review addresses the need to investigate the role of protein phosphorylation in zinc transporter function and regulation, and argues for a pressing need to introduce quantitative phosphoproteomics to specifically target zinc transporters and proteins involved in zinc signaling. Finally, different quantitative phosphoproteomic strategies are suggested.
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Affiliation(s)
- T E Thingholm
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, J.B. Winsløws Vej 25, 3, 5000, Odense C, Denmark.
| | - L Rönnstrand
- Division of Translational Cancer Research, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Lund Stem Cell Center, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - P A Rosenberg
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Neurology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
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30
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Bensimon A, Koch JP, Francica P, Roth SM, Riedo R, Glück AA, Orlando E, Blaukat A, Aebersold DM, Zimmer Y, Aebersold R, Medová M. Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics. Mol Oncol 2020; 14:1185-1206. [PMID: 32336009 PMCID: PMC7266272 DOI: 10.1002/1878-0261.12696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that interference with growth factor receptor tyrosine kinase (RTK) signaling can affect DNA damage response (DDR) networks, with a consequent impact on cellular responses to DNA‐damaging agents widely used in cancer treatment. In that respect, the MET RTK is deregulated in abundance and/or activity in a variety of human tumors. Using two proteomic techniques, we explored how disrupting MET signaling modulates global cellular phosphorylation response to ionizing radiation (IR). Following an immunoaffinity‐based phosphoproteomic discovery survey, we selected candidate phosphorylation sites for extensive characterization by targeted proteomics focusing on phosphorylation sites in both signaling networks. Several substrates of the DDR were confirmed to be modulated by sequential MET inhibition and IR, or MET inhibition alone. Upon combined treatment, for two substrates, NUMA1 S395 and CHEK1 S345, the gain and loss of phosphorylation, respectively, were recapitulated using invivo tumor models by immunohistochemistry, with possible utility in future translational research. Overall, we have corroborated phosphorylation sites at the intersection between MET and the DDR signaling networks, and suggest that these represent a class of proteins at the interface between oncogene‐driven proliferation and genomic stability.
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Affiliation(s)
- Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland
| | - Jonas P Koch
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Paola Francica
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Selina M Roth
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Rahel Riedo
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Astrid A Glück
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Eleonora Orlando
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Andree Blaukat
- Global Research & Development, Merck KGaA, Darmstadt, Germany
| | - Daniel M Aebersold
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Yitzhak Zimmer
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland.,Faculty of Science, University of Zürich, Switzerland
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
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31
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Medo M, Aebersold DM, Medová M. ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data. BMC Bioinformatics 2019; 20:563. [PMID: 31706265 PMCID: PMC6842221 DOI: 10.1186/s12859-019-3144-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Background Data from discovery proteomic and phosphoproteomic experiments typically include missing values that correspond to proteins that have not been identified in the analyzed sample. Replacing the missing values with random numbers, a process known as “imputation”, avoids apparent infinite fold-change values. However, the procedure comes at a cost: Imputing a large number of missing values has the potential to significantly impact the results of the subsequent differential expression analysis. Results We propose a method that identifies differentially expressed proteins by ranking their observed changes with respect to the changes observed for other proteins. Missing values are taken into account by this method directly, without the need to impute them. We illustrate the performance of the new method on two distinct datasets and show that it is robust to missing values and, at the same time, provides results that are otherwise similar to those obtained with edgeR which is a state-of-art differential expression analysis method. Conclusions The new method for the differential expression analysis of proteomic data is available as an easy to use Python package.
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Affiliation(s)
- Matúš Medo
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, 3010, Switzerland. .,Department for BioMedical Research, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland. .,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, PR China. .,Department of Physics, University of Fribourg, Fribourg, 1700, Switzerland.
| | - Daniel M Aebersold
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, 3010, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, 3010, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
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32
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Rahm M, Merl-Pham J, Adamski J, Hauck SM. Time-resolved phosphoproteomic analysis elucidates hepatic 11,12-Epoxyeicosatrienoic acid signaling pathways. Prostaglandins Other Lipid Mediat 2019; 146:106387. [PMID: 31669255 DOI: 10.1016/j.prostaglandins.2019.106387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/24/2019] [Accepted: 10/16/2019] [Indexed: 01/20/2023]
Abstract
Epoxyeicosatrienoic acids (EETs) are potent lipid mediators with well-established effects in vascular tissues. Recent studies indicated an emerging role of these eicosanoids in metabolic diseases and the EET signaling pathway was shown to be involved in hepatic insulin sensitivity. However, compared to vascular tissues, there is only limited knowledge about the underlying signaling pathways in the liver. Therefore, we employed an LC-MS/MS-based time-resolved phosphoproteomics approach to characterize 11,12-EET-mediated signaling events in the liver cell line Hepa 1-6. 11,12-EET treatment resulted in the time-dependent regulation of phosphopeptides involved in processes as yet unknown to be affected by EETs, including RNA processing, splicing and translation regulation. Pathway analysis combined with western blot-based validation revealed enhanced AKT/mTOR/p70S6K signaling as demonstrated by increased acute phosphorylation of AKT (Ser473) and p70S6K (Thr389). In addition, 11,12-EET treatment led to differential regulation of phosphopeptides including important mediators of the DNA damage response and we observed a prolonged induction of the etoposide-induced DNA damage marker γH2AX in response to 11,12-EET. In summary, our findings extend current knowledge of 11,12-EET signaling events and emphasize the importance of the AKT/mTOR/p70S6K pathway in hepatic 11,12-EET signaling. Based on the results presented in this study, we furthermore propose a novel role of EET signaling in the regulation of the DNA damage response.
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Affiliation(s)
- Marco Rahm
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany.
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33
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34
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Cutolo E, Parvin N, Ruge H, Pirayesh N, Roustan V, Weckwerth W, Teige M, Grieco M, Larosa V, Vothknecht UC. The High Light Response in Arabidopsis Requires the Calcium Sensor Protein CAS, a Target of STN7- and STN8-Mediated Phosphorylation. FRONTIERS IN PLANT SCIENCE 2019; 10:974. [PMID: 31417591 PMCID: PMC6682602 DOI: 10.3389/fpls.2019.00974] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/11/2019] [Indexed: 05/18/2023]
Abstract
Reversible phosphorylation of thylakoid proteins contributes to photoacclimation responses in photosynthetic organisms, enabling the fine-tuning of light harvesting under changing light conditions and promoting the onset of photoprotective processes. However, the precise functional role of many of the described phosphorylation events on thylakoid proteins remains elusive. The calcium sensor receptor protein (CAS) has previously been indicated as one of the targets of the state transition kinase 8 (STN8). Here we show that in Arabidopsis thaliana, CAS is also phosphorylated by the state transition kinase 7 (STN7), as well as by another, so-far unknown, Ca2+-dependent kinase. Phosphoproteomics analysis and in vitro phosphorylation assays on CAS variants identified the phylogenetically conserved residues Thr-376, Ser-378, and Thr-380 as the major phosphorylation sites of the STN kinases. Spectroscopic analyses of chlorophyll fluorescence emission at 77K further showed that, while the cas mutant is not affected in state transition, it displays a persistent strong excitation of PSI under high light exposure, similar to the phenotype previously observed in other mutants defective in photoacclimation mechanisms. Together with the observation of a strong concomitant phosphorylation of light harvesting complex II (LHCII) and photosynthetic core proteins under high irradiance in the cas mutant this suggests a role for CAS in the STN7/STN8/TAP38 network of phosphorylation-mediated photoacclimation processes in Arabidopsis.
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Affiliation(s)
- Edoardo Cutolo
- Plant Cell Biology, Institut für Zelluläre und Molekulare Botanik, University of Bonn, Bonn, Germany
| | - Nargis Parvin
- Department of Plant Nutrition, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz, University of Bonn, Bonn, Germany
| | - Henning Ruge
- Department of Biology I, Ludwig Maximilian University of Munich, Munich, Germany
| | - Niloufar Pirayesh
- Plant Cell Biology, Institut für Zelluläre und Molekulare Botanik, University of Bonn, Bonn, Germany
| | - Valentin Roustan
- Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Markus Teige
- Department of Molecular Systems Biology, University of Vienna, Vienna, Austria
| | - Michele Grieco
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Veronique Larosa
- Laboratory of Genetics and Physiology of Microalgae, InBios, University of Liège, Liège, Belgium
| | - Ute C. Vothknecht
- Plant Cell Biology, Institut für Zelluläre und Molekulare Botanik, University of Bonn, Bonn, Germany
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35
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Liu M, Torsetnes SB, Wierzbicka C, Jensen ON, Sellergren B, Irgum K. Selective Enrichment of Phosphorylated Peptides by Monolithic Polymers Surface Imprinted with bis-Imidazolium Moieties by UV-Initiated Cryopolymerization. Anal Chem 2019; 91:10188-10196. [DOI: 10.1021/acs.analchem.9b02211] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mingquan Liu
- Umeå University, Department of Chemistry, S-901 87 Umeå, Sweden
| | - Silje Bøen Torsetnes
- University of Southern Denmark, Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, Campusvej 55, DK-5230 Odense M, Denmark
| | - Celina Wierzbicka
- Malmö University, Department of Biomedical Sciences, Faculty of Health and Society, S-205 06 Malmö, Sweden
| | - Ole Nørregaard Jensen
- University of Southern Denmark, Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, Campusvej 55, DK-5230 Odense M, Denmark
| | - Börje Sellergren
- Malmö University, Department of Biomedical Sciences, Faculty of Health and Society, S-205 06 Malmö, Sweden
| | - Knut Irgum
- Umeå University, Department of Chemistry, S-901 87 Umeå, Sweden
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36
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Affiliation(s)
- Karl W Barber
- Department of Cellular and Molecular Physiology and the Systems Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and the Systems Biology Institute, Yale University, West Haven, Connecticut, USA
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37
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Wang J, Wang Z, Sun N, Deng C. Immobilization of titanium dioxide/ions on magnetic microspheres for enhanced recognition and extraction of mono- and multi-phosphopeptides. Mikrochim Acta 2019; 186:236. [PMID: 30868259 DOI: 10.1007/s00604-019-3346-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/27/2019] [Indexed: 11/25/2022]
Abstract
The authors are presenting a novel strategy for global phosphoproteome recognition in practical samples. It integrates metal oxide affinity chromatography (MOAC) and immobilization metal ion affinity chromatography (IMAC). This resulted in a kind of titanium dioxide/ion-based multifunctional probe (dubbed T2M). The T2M combines the features of MOAC and IMAC including their recognition preferences towards mono- and multi-phosphorylated peptides. Hence, they exhibit an outstanding recognition capability towards global phosphoproteome, high sensitivity (the limit of detection of which is merely 10 fmol) and excellent specificity in MALDI-TOF MS detection. Their performance is further demonstrated by the identification of the phosphoproteome in non-fat milk and human saliva. By combining T2M with nano LC-MS/MS, remarkable results are obtained in the tryptic digestion of healthy eye lens and cataract lens phosphoproteomes. A total of 658 and 162 phosphopeptides, respectively, were identified. This indicates that phosphorylation and the appearance of cataract can be related to each other. Graphical abstract Schematic presentation of the preparation of titanium dioxide/ion-based multifunctional magnetic nanomaterials (T2M). The T2M based enrichment protocol exhibits outstanding recognition capability towards global phosphoproteome. This protocol shows great prospect for clarifying mechanism of phosphorylation-related diseases via further information acquisition.
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Affiliation(s)
- Jiawen Wang
- Department of Chemistry and The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200433, China
| | - Zidan Wang
- Department of Chemistry and The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200433, China
| | - Nianrong Sun
- Department of Chemistry and The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200433, China.
| | - Chunhui Deng
- Department of Chemistry and The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200433, China.
- Institutes of Biomedical Sciences and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
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38
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Yakubu RR, Nieves E, Weiss LM. The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:169-198. [PMID: 31347048 DOI: 10.1007/978-3-030-15950-4_10] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass Spectrometry (MS) has revolutionized the way we study biomolecules, especially proteins, their interactions and posttranslational modifications (PTM). As such MS has established itself as the leading tool for the analysis of PTMs mainly because this approach is highly sensitive, amenable to high throughput and is capable of assigning PTMs to specific sites in the amino acid sequence of proteins and peptides. Along with the advances in MS methodology there have been improvements in biochemical, genetic and cell biological approaches to mapping the interactome which are discussed with consideration for both the practical and technical considerations of these techniques. The interactome of a species is generally understood to represent the sum of all potential protein-protein interactions. There are still a number of barriers to the elucidation of the human interactome or any other species as physical contact between protein pairs that occur by selective molecular docking in a particular spatiotemporal biological context are not easily captured and measured.PTMs massively increase the complexity of organismal proteomes and play a role in almost all aspects of cell biology, allowing for fine-tuning of protein structure, function and localization. There are an estimated 300 PTMS with a predicted 5% of the eukaryotic genome coding for enzymes involved in protein modification, however we have not yet been able to reliably map PTM proteomes due to limitations in sample preparation, analytical techniques, data analysis, and the substoichiometric and transient nature of some PTMs. Improvements in proteomic and mass spectrometry methods, as well as sample preparation, have been exploited in a large number of proteome-wide surveys of PTMs in many different organisms. Here we focus on previously published global PTM proteome studies in the Apicomplexan parasites T. gondii and P. falciparum which offer numerous insights into the abundance and function of each of the studied PTM in the Apicomplexa. Integration of these datasets provide a more complete picture of the relative importance of PTM and crosstalk between them and how together PTM globally change the cellular biology of the Apicomplexan protozoa. A multitude of techniques used to investigate PTMs, mostly techniques in MS-based proteomics, are discussed for their ability to uncover relevant biological function.
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Affiliation(s)
- Rama R Yakubu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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Hoedt E, Zhang G, Neubert TA. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:531-539. [PMID: 31347069 DOI: 10.1007/978-3-030-15950-4_31] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
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Thawornpan P, Thanapongpichat S, Tun AW, Phongdara A, de Jong L, Buncherd H. Fly-ash as a low-cost material for isolation of phosphoproteins. CHEMOSPHERE 2018; 213:124-132. [PMID: 30216812 DOI: 10.1016/j.chemosphere.2018.08.150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Metal oxide affinity chromatography (MOAC) is one of the most commonly used techniques for selective isolation phosphoproteins and phosphopeptides. This technique is capable of capturing the phosphorylated biomolecules through the affinity of the phosphoryl group for metal oxides/hydroxides. Fly-ash (FA), a by-product of coal-combustion power plants, is primarily composed of oxides of silicon and metals, among which iron and titanium. A number of studies have demonstrated the potential of these metal oxides for phosphoprotein and phosphopeptide enrichment. FA is annually produced over hundred million tons worldwide and generally considered as hazardous waste. It is thus of great importance to enhance its utilization. Here we present the first demonstration of the utility of FA as a low-cost MOAC material for the enrichment of phosphoproteins. With an FA-microcolumn, phosphoproteins can be successfully sequestered from other proteins. FA-microcolumns are shown to be simple, cheap and selective devices for phosphoprotein enrichment from a small volume of mixtures.
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Affiliation(s)
- Pongsakorn Thawornpan
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | | | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Thailand
| | - Amornrat Phongdara
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand; Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Luitzen de Jong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, the Netherlands
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand.
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Baro B, Játiva S, Calabria I, Vinaixa J, Bech-Serra JJ, de LaTorre C, Rodrigues J, Hernáez ML, Gil C, Barceló-Batllori S, Larsen MR, Queralt E. SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast. Gigascience 2018; 7:4982941. [PMID: 29688323 PMCID: PMC5967524 DOI: 10.1093/gigascience/giy047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 04/18/2018] [Indexed: 01/12/2023] Open
Abstract
Background Protein phosphatase 2A (PP2A) is a family of conserved serine/threonine phosphatases involved in several essential aspects of cell growth and proliferation. PP2ACdc55 phosphatase has been extensively related to cell cycle events in budding yeast; however, few PP2ACdc55 substrates have been identified. Here, we performed a quantitative mass spectrometry approach to reveal new substrates of PP2ACdc55 phosphatase and new PP2A-related processes in mitotic arrested cells. Results We identified 62 statistically significant PP2ACdc55 substrates involved mainly in actin-cytoskeleton organization. In addition, we validated new PP2ACdc55 substrates such as Slk19 and Lte1, involved in early and late anaphase pathways, and Zeo1, a component of the cell wall integrity pathway. Finally, we constructed docking models of Cdc55 and its substrate Mob1. We found that the predominant interface on Cdc55 is mediated by a protruding loop consisting of residues 84–90, thus highlighting the relevance of these aminoacids for substrate interaction. Conclusions We used phosphoproteomics of Cdc55-deficient cells to uncover new PP2ACdc55 substrates and functions in mitosis. As expected, several hyperphosphorylated proteins corresponded to Cdk1-dependent substrates, although other kinases’ consensus motifs were also enriched in our dataset, suggesting that PP2ACdc55 counteracts and regulates other kinases distinct from Cdk1. Indeed, Pkc1 emerged as a novel node of PP2ACdc55 regulation, highlighting a major role of PP2ACdc55 in actin cytoskeleton and cytokinesis, gene ontology terms significantly enriched in the PP2ACdc55-dependent phosphoproteome.
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Affiliation(s)
- Barbara Baro
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Soraya Játiva
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Inés Calabria
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Judith Vinaixa
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joan-Josep Bech-Serra
- IDIBELL Proteomics Unit, Institut d'Investigacions Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Carolina de LaTorre
- IDIBELL Proteomics Unit, Institut d'Investigacions Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - João Rodrigues
- Structural Biology Department, School of Medicine, Stanford, California, USA
| | - María Luisa Hernáez
- Proteomics Unit, Parque Científico de Madrid, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Concha Gil
- Proteomics Unit, Parque Científico de Madrid, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Silvia Barceló-Batllori
- IDIBELL Proteomics Unit, Institut d'Investigacions Biomèdica de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, Odense M, Denmark
| | - Ethel Queralt
- Cell Cycle Group, Cancer Epigenetics and Biology Program, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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Cheng LC, Li Z, Graeber TG, Graham NA, Drake JM. Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate Cancer. J Vis Exp 2018. [PMID: 30124664 PMCID: PMC6126612 DOI: 10.3791/57996] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phosphoproteomics involves the large-scale study of phosphorylated proteins. Protein phosphorylation is a critical step in many signal transduction pathways and is tightly regulated by kinases and phosphatases. Therefore, characterizing the phosphoproteome may provide insights into identifying novel targets and biomarkers for oncologic therapy. Mass spectrometry provides a way to globally detect and quantify thousands of unique phosphorylation events. However, phosphopeptides are much less abundant than non-phosphopeptides, making biochemical analysis more challenging. To overcome this limitation, methods to enrich phosphopeptides prior to the mass spectrometry analysis are required. We describe a procedure to extract and digest proteins from tissue to yield peptides, followed by an enrichment for phosphotyrosine (pY) and phosphoserine/threonine (pST) peptides using an antibody-based and/or titanium dioxide (TiO2)-based enrichment method. After the sample preparation and mass spectrometry, we subsequently identify and quantify phosphopeptides using liquid chromatography-mass spectrometry and analysis software.
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Affiliation(s)
- Larry C Cheng
- Graduate Program in Cellular and Molecular Pharmacology, School of Graduate Studies, Rutgers University, The State University of New Jersey; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, The State University of New Jersey
| | - Zhen Li
- Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School
| | - Thomas G Graeber
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, Jonsson Comprehensive Cancer Center, UCLA Metabolomics Center, and California NanoSystems Institute, David Geffen School of Medicine, University of California, Los Angeles
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California
| | - Justin M Drake
- Graduate Program in Cellular and Molecular Pharmacology, School of Graduate Studies, Rutgers University, The State University of New Jersey; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, The State University of New Jersey; Department of Medicine, Division of Medical Oncology, Rutgers Robert Wood Johnson Medical School; Pharmacology, Rutgers Robert Wood Johnson Medical School; Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey;
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Marmelstein AM, Morgan JAM, Penkert M, Rogerson DT, Chin JW, Krause E, Fiedler D. Pyrophosphorylation via selective phosphoprotein derivatization. Chem Sci 2018; 9:5929-5936. [PMID: 30079207 PMCID: PMC6050540 DOI: 10.1039/c8sc01233d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/08/2018] [Indexed: 01/13/2023] Open
Abstract
An important step in elucidating the function of protein post-translational modifications (PTMs) is gaining access to site-specifically modified, homogeneous samples for biochemical characterization. Protein pyrophosphorylation is a poorly characterized PTM, and here a chemical approach to obtain pyrophosphoproteins is reported. Photo-labile phosphorimidazolide reagents were developed for selective pyrophosphorylation, affinity-capture, and release of pyrophosphoproteins. Kinetic analysis of the reaction revealed rate constants between 9.2 × 10-3 to 0.58 M-1 s-1, as well as a striking proclivity of the phosphorimidazolides to preferentially react with phosphate monoesters over other nucleophilic side chains. Besides enabling the characterization of pyrophosphorylation on protein function, this work highlights the utility of phosphoryl groups as handles for selective protein modification for a variety of applications, such as phosphoprotein bioconjugation and enrichment.
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Affiliation(s)
- Alan M Marmelstein
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Department of Chemistry , Princeton University , Washington Road , Princeton , New Jersey 08544 , USA
| | - Jeremy A M Morgan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
| | - Martin Penkert
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Institut für Chemie , Humboldt Universität zu Berlin , Brook-Taylor-Str. 2 , 12489 Berlin , Germany
| | - Daniel T Rogerson
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge , UK
| | - Eberhard Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie , Robert-Rössle Str. 10 , 13125 Berlin , Germany .
- Institut für Chemie , Humboldt Universität zu Berlin , Brook-Taylor-Str. 2 , 12489 Berlin , Germany
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Paulo JA, Navarrete-Perea J, Erickson AR, Knott J, Gygi SP. An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1505-1511. [PMID: 29671274 PMCID: PMC6004253 DOI: 10.1007/s13361-018-1946-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 06/08/2023]
Abstract
Phosphorylation-mediated signaling pathways have major implications in cellular regulation and disease. However, proteins with roles in these pathways are frequently less abundant and phosphorylation is often sub-stoichiometric. As such, the efficient enrichment, and subsequent recovery of phosphorylated peptides, is vital. Mass spectrometry-based proteomics is a well-established approach for quantifying thousands of phosphorylation events in a single experiment. We designed a peptide internal standard-based assay directed toward sample preparation strategies for mass spectrometry analysis to understand better phosphopeptide recovery from enrichment strategies. We coupled mass-differential tandem mass tag (mTMT) reagents (specifically, TMTzero and TMTsuper-heavy), nine mass spectrometry-amenable phosphopeptides (phos9), and peak area measurements from extracted ion chromatograms to determine phosphopeptide recovery. We showcase this mTMT/phos9 recovery assay by evaluating three phosphopeptide enrichment workflows. Our assay provides data on the recovery of phosphopeptides, which complement other metrics, namely the number of identified phosphopeptides and enrichment specificity. Our mTMT/phos9 assay is applicable to any enrichment protocol in a typical experimental workflow irrespective of sample origin or labeling strategy. Graphical Abstract ᅟ.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
| | - Jose Navarrete-Perea
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | - Alison R Erickson
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA
| | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA, 02115, USA.
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Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. J Proteome Res 2018; 17:2226-2236. [PMID: 29734811 DOI: 10.1021/acs.jproteome.8b00217] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry (MS) coupled toisobaric labeling has developed rapidly into a powerful strategy for high-throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and, by inference, thousands of proteins from multiple samples in a single MS experiment. Accurate quantification demands a consistent and robust sample-preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of tandem mass tag (TMT)-labeled proteins and phosphopeptides that we have named the streamlined (SL)-TMT protocol. We describe a universally applicable strategy that requires minimal individual sample processing and permits the seamless addition of a phosphopeptide enrichment step ("mini-phos") with little deviation from the deep proteome analysis. To showcase our workflow, we profile the proteome of wild-type Saccharomyces cerevisiae yeast grown with either glucose or pyruvate as the carbon source. Here, we have established a streamlined TMT protocol that enables deep proteome and medium-scale phosphoproteome analysis.
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Affiliation(s)
- José Navarrete-Perea
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Qing Yu
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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Zhou J. Phosphopeptide enrichment with cross-linked Os(II)(dmebpy) 2 Cl-derivatized acrylamide and vinylimidazole copolymer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1-8. [PMID: 28884863 DOI: 10.1002/rcm.7985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Reversible phosphorylation of proteins catalyzed by kinases and phosphatases plays a key regulatory role in intracellular biological processes. Protein phosphorylation profiling is still a challenge due to its low stoichiometry, diversity of phosphorylated protein forms, and dynamic nature of phosphorylation states. Mass spectrometry (MS) has been widely used for the characterization of protein phosphorylation, due to its high sensitivity and MS/MS sequencing capability. However, the low abundance and ionization efficiency of phosphorylated peptides and interference from their non-phosphorylated counterparts and other peptides in the enzymatic digests of proteins complicate the localization of phosphorylation sites in liquid chromatography (LC)/MS analysis. So the enrichment of phosphopeptides from the digests is often required before LC/MS. Immobilized metal affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC) are the two most commonly used enrichment techniques for phosphopeptides prior to MS analysis. METHODS Cross-linked Os(II)(4,4'-dimethyl-2,2'-bipyridine)2 Cl-derivatized acrylamide and vinylimidazole copolymer were applied for the enrichment of phosphopeptides. RESULTS Under neutral loading buffer conditions phosphopeptides bind on the Os-polymer without nonspecific binding of acidic peptides. Differential binding of monophosphorylated and multiply phosphorylated peptides can be achieved under different concentrations of imidazole. Sequential elution of bound phosphopeptides can be obtained with elution buffers of different pH values below 3. The loading buffers with imidazole can be aqueous or 7/3 H2 O/ACN. Once phosphopeptides bind onto the Os-polymer, washing with water, 0.1% acetic acid (pH ~ 3) or 1/1 H2 O/ACN 0.05% acetic acid (pH ~3) does not elute phosphopeptides. The Os-polymer does not show bias of binding and elution toward phosphopeptide standards with singly, doubly and triply phosphorylated sites. CONCLUSIONS Cross-linked Os(II)(dimethylbipyridine)2 Cl-derivatized poly(acrylamide)-poly(vinylimidazole) copolymer is proven to be a new efficient IMAC resin for phosphopeptide enrichment and shows some unique properties for differential binding and sequential elution of phosphopeptides. It could become a better alternative to traditional IMAC and TiO2 for phosphopeptide enrichment.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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Roustan V, Weckwerth W. Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2018; 9:1590. [PMID: 30546371 PMCID: PMC6280106 DOI: 10.3389/fpls.2018.01590] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 10/15/2018] [Indexed: 05/13/2023]
Abstract
Rapamycin is an inhibitor of the evolutionary conserved Target of Rapamycin (TOR) kinase which promotes and coordinates translation with cell growth and division. In heterotrophic organisms, TOR regulation is based on intra- and extracellular stimuli such as amino acids level and insulin perception. However, how plant TOR pathways have evolved to integrate plastid endosymbiosis is a remaining question. Despite the close association of the TOR signaling with the coordination between protein turn-over and growth, proteome and phosphoproteome acclimation to a rapamycin treatment have not yet been thoroughly investigated in Chlamydomonas reinhardtii. In this study, we have used in vivo label-free phospho-proteomic analysis to profile both protein and phosphorylation changes at 0, 24, and 48 h in Chlamydomonas cells treated with rapamycin. Using multivariate statistics we highlight the impact of TOR inhibition on both the proteome and the phosphoproteome. Two-way ANOVA distinguished differential levels of proteins and phosphoproteins in response either to culture duration and rapamycin treatment or combined effects. Finally, protein-protein interaction networks and functional enrichment analysis underlined the relation between plastid and mitochondrial metabolism. Prominent changes of proteins involved in sulfur, cysteine, and methionine as well as nucleotide metabolism on the one hand, and changes in the TCA cycle on the other highlight the interplay of chloroplast and mitochondria metabolism. Furthermore, TOR inhibition revealed changes in the endomembrane trafficking system. Phosphoproteomics data, on the other hand, highlighted specific differentially regulated phosphorylation sites for calcium-regulated protein kinases as well as ATG7, S6K, and PP2C. To conclude we provide a first combined Chlamydomonas proteomics and phosphoproteomics dataset in response to TOR inhibition, which will support further investigations.
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Affiliation(s)
- Valentin Roustan
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- *Correspondence: Wolfram Weckwerth,
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50
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Yang SS, Yu HX, Wang ZZ, Liu HL, Zhang H, Yu X, Shang W, Chen GQ, Gu ZY. An Exfoliated 2D Egyptian Blue Nanosheet for Highly Selective Enrichment of Multi-phosphorylated Peptides in Mass Spectrometric Analysis. Chemistry 2017; 24:2109-2116. [DOI: 10.1002/chem.201704138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hai-Xia Yu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Zi-Zhen Wang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hai-Long Liu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hao Zhang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine; Nanjing University of, Chinese Medicine; 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
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center; Nanjing University; 12 Xuefu Avenue Nanjing 210061 China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
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