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Zhang Y, Pan Y, Liu W, Zhou YJ, Wang K, Wang L, Sohail M, Ye M, Zou H, Zhao ZK. In vivo protein allylation to capture protein methylation candidates. Chem Commun (Camb) 2017; 52:6689-92. [PMID: 27115613 DOI: 10.1039/c6cc02386j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An approach combining in vivo protein allylation, chemical tagging and affinity enrichment was devised to capture protein methylation candidates in yeast S. cerevisiae. The study identified 167 hits, covering many proteins with known methylation events on different types of amino acid residues.
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Affiliation(s)
- Yixin Zhang
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Yanbo Pan
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Wujun Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Keyun Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Lei Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Muhammad Sohail
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Hanfa Zou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Zongbao K Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China. and State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China
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2
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White FM, Wolf-Yadlin A. Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:295-315. [PMID: 27049636 DOI: 10.1146/annurev-anchem-071015-041542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein phosphorylation-mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks.
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Affiliation(s)
- Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
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3
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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4
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Liu C, Topchiy E, Lehmann T, Basile F. Characterization of the dehydration products due to thermal decomposition of peptides by liquid chromatography-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:625-632. [PMID: 25800200 DOI: 10.1002/jms.3570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/30/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Thermal decomposition (TD) of proteins is being investigated as a rapid digestion step for bottom-up proteomics. Mass spectrometry (MS) analyses of the TD products of simple peptides and intact proteins have revealed several nonvolatile products at masses lower than the precursor biomolecule (M). In addition to products stemming from site-specific cleavages, many signals are also observed at a corresponding M-18, most likely because of dehydration (M-H2O) during the heating process. Understanding the structural nature of the water loss product is important in establishing the utility of their tandem mass spectra (collision-induced dissociation) in determining the precursor ion amino acid sequence in a bottom-up proteomic workflow. Dehydration of a peptide can take place from a variety of sources including side chain groups, C-terminus, and/or intramolecular cyclization (C to N-terminus cyclization). In this work, liquid chromatography-tandem MS (LC-MS/MS) and a series of standard peptides (angiotensin II, DRVYIHPF and its cyclic analog) are implemented to decipher the structure of the TD dehydration product. In addition, a derivatization strategy incorporating N-terminus acetylation was developed that allowed the direct comparison of tandem mass spectra of standard cyclic peptides with those resulting from the TD process, thus eliminating any ambiguity from the direct comparison of their mass spectra (due to gas-phase cyclization of b-ions, which can result in sequence scrambling of the precursor ion). Results from these investigations indicated that peptide dehydrated TD products were mostly linear in nature, and water loss was favored from the C-terminus carboxyl group or, when present, the aspartic acid side chain. Given the predictable nature of the formation of TD dehydration products, their MS/MS analysis can be of utility in providing complementary and confirmatory sequence information of the precursor peptide.
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Affiliation(s)
- Chenglin Liu
- Department of Chemistry, University of Wyoming, Laramie, WY, 82071, USA
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5
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N- and O-acetylation of threonine residues in the context of proteomics. J Proteomics 2014; 108:369-72. [DOI: 10.1016/j.jprot.2014.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/07/2014] [Accepted: 06/09/2014] [Indexed: 11/20/2022]
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6
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Britton LMP, Newhart A, Bhanu NV, Sridharan R, Gonzales-Cope M, Plath K, Janicki SM, Garcia BA. Initial characterization of histone H3 serine 10 O-acetylation. Epigenetics 2013; 8:1101-13. [PMID: 23949383 DOI: 10.4161/epi.26025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In eukaryotic organisms, histone posttranslational modifications (PTMs) are indispensable for their role in maintaining cellular physiology, often through their mediation of chromatin-related processes such as transcription. Targeted investigations of this ever expanding network of chemical moieties continue to reveal genetic, biochemical, and cellular nuances of this complex landscape. In this study, we present our findings on a novel class of histone PTMs: Serine, Threonine, and Tyrosine O-acetylation. We have combined highly sensitive nano-LC-MS/MS experiments and immunodetection assays to identify and validate these unique marks found only on histone H3. Mass spectrometry experiments have determined that several of these O-acetylation marks are conserved in many species, ranging from yeast to human. Additionally, our investigations reveal that histone H3 serine 10 acetylation (H3S10ac) is potentially linked to cell cycle progression and cellular pluripotency. Here, we provide a glimpse into the functional implications of this H3-specific histone mark, which may be of high value for further studies of chromatin.
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Affiliation(s)
- Laura-Mae P Britton
- Department of Molecular Biology; Princeton University; Princeton, NJ USA; Epigenetics Program; Department of Biochemistry and Biophysics; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
| | - Alyshia Newhart
- Molecular and Cellular Oncogenesis Program; The Wistar Institute; Philadelphia, PA USA
| | - Natarajan V Bhanu
- Epigenetics Program; Department of Biochemistry and Biophysics; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
| | - Rupa Sridharan
- University of California Los Angeles; David Geffen School of Medicine; Department of Biological Chemistry; Jonsson Comprehensive Cancer Center; Molecular Biology Institute; Bioinformatics Interdepartmental Degree Program; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; Los Angeles, CA USA; Current affiliation: Wisconsin Institute for Discovery; Department of Cell and Regenerative Biology; University of Wisconsin; Madison, WI USA
| | - Michelle Gonzales-Cope
- Department of Molecular Biology; Princeton University; Princeton, NJ USA; Epigenetics Program; Department of Biochemistry and Biophysics; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
| | - Kathrin Plath
- University of California Los Angeles; David Geffen School of Medicine; Department of Biological Chemistry; Jonsson Comprehensive Cancer Center; Molecular Biology Institute; Bioinformatics Interdepartmental Degree Program; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; Los Angeles, CA USA
| | - Susan M Janicki
- Molecular and Cellular Oncogenesis Program; The Wistar Institute; Philadelphia, PA USA
| | - Benjamin A Garcia
- Epigenetics Program; Department of Biochemistry and Biophysics; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
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Huang X, Huang L, Peng H, Guru A, Xue W, Hong SY, Liu M, Sharma S, Fu K, Caprez AP, Swanson DR, Zhang Z, Ding SJ. ISPTM: an iterative search algorithm for systematic identification of post-translational modifications from complex proteome mixtures. J Proteome Res 2013; 12:3831-42. [PMID: 23919725 DOI: 10.1021/pr4003883] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear matrix proteins with unknown modifications. ISPTM revealed that many chemical PTMs were introduced by urea and iodoacetamide during sample preparation and many biological PTMs, including dimethylation of arginine and lysine, were significantly activated by Adriamycin treatment in nuclear matrix associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification compared with that of the conventional all-in-one search approach, and offered PTM identification results that were complementary to InsPecT and MODa, both of which are established PTM identification algorithms. In summary, ISPTM is a new and powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures.
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Affiliation(s)
- Xin Huang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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8
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Arnaudo AM, Garcia BA. Proteomic characterization of novel histone post-translational modifications. Epigenetics Chromatin 2013; 6:24. [PMID: 23916056 PMCID: PMC3737111 DOI: 10.1186/1756-8935-6-24] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/01/2013] [Indexed: 11/10/2022] Open
Abstract
Histone post-translational modifications (PTMs) have been linked to a variety of biological processes and disease states, thus making their characterization a critical field of study. In the last 5 years, a number of novel sites and types of modifications have been discovered, greatly expanding the histone code. Mass spectrometric methods are essential for finding and validating histone PTMs. Additionally, novel proteomic, genomic and chemical biology tools have been developed to probe PTM function. In this snapshot review, proteomic tools for PTM identification and characterization will be discussed and an overview of PTMs found in the last 5 years will be provided.
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Affiliation(s)
- Anna M Arnaudo
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine University of Pennsylvania, 1009C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA.
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9
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Computer aided manual validation of mass spectrometry-based proteomic data. Methods 2013; 61:219-26. [PMID: 23500044 DOI: 10.1016/j.ymeth.2013.03.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/28/2013] [Accepted: 03/04/2013] [Indexed: 11/23/2022] Open
Abstract
Advances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design. Manual validation is the gold standard approach to confirm accuracy of database identifications, but is extremely time-intensive. To palliate the increasing time required to manually validate large proteomic datasets, we provide computer aided manual validation software (CAMV) to expedite the process. Relevant spectra are collected, catalogued, and pre-labeled, allowing users to efficiently judge the quality of each identification and summarize applicable quantitative information. CAMV significantly reduces the burden associated with manual validation and will hopefully encourage broader adoption of manual validation in mass spectrometry-based proteomics.
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Lee S, Tan M, Dai L, Kwon OK, Yang JS, Zhao Y, Chen Y. MS/MS of Synthetic Peptide Is Not Sufficient to Confirm New Types of Protein Modifications. J Proteome Res 2013; 12:1007-13. [DOI: 10.1021/pr300667e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sangkyu Lee
- College of Pharmacy, Research Institute of
Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701, Korea
| | - Minjia Tan
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lunzhi Dai
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Oh Kwang Kwon
- College of Pharmacy, Research Institute of
Pharmaceutical Sciences, Kyungpook National University, Daegu 702-701, Korea
| | - Jeong Soo Yang
- Clinical Trial Center, Samsung Medical Center, Seoul
135-710, South Korea
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yue Chen
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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11
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Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011; 146:1016-28. [PMID: 21925322 DOI: 10.1016/j.cell.2011.08.008] [Citation(s) in RCA: 1277] [Impact Index Per Article: 98.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 05/25/2011] [Accepted: 08/05/2011] [Indexed: 12/16/2022]
Abstract
We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells.
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12
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Zhang J, Al-Eryani R, Ball HL. Mass spectrometry analysis of 2-nitrophenylhydrazine carboxy derivatized peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1958-1967. [PMID: 21952763 DOI: 10.1007/s13361-011-0220-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 07/14/2011] [Accepted: 07/19/2011] [Indexed: 05/31/2023]
Abstract
Peptides with two or more basic residues, including those with post-translational modifications (PTMs), such as methylation and phosphorylation, can be highly hydrophilic and, therefore, are often difficult to be retained on a reversed-phase (RP) column. In addition, these highly hydrophilic peptides may carry two or more positive charges, which often fragment poorly upon collisionally activated dissociation (CAD), resulting in few sequence-specific ions. C-terminal rearrangement may also occur during CAD. Furthermore, some PTMs are labile and tend to be lost when subjected to CAD as is the case with phosphorylation on serine or threonine. To overcome the difficulties of separation, detection, and fragmentation of highly hydrophilic peptides, we report here the effect of carboxy group derivatization with 2-nitrophenylhydrazine (this strategy will be called NPHylation for simplicity). NPHylation significantly increases the hydrophobicity of the peptides, eliminates C-terminal rearrangement in all cases, and offers enhanced sensitivity in some cases. In addition, the CAD spectra of the resulting NPHylated peptides carry more sequence-specific ions due to significant reduction of sequence scrambling as observed for peptide EHAGVISVL. Furthermore, the different carboxy derivatives of this peptide undergo sequence scrambling to varying degrees, which clearly demonstrates that the C-terminus has a profound effect on peptide fragmentation. Finally, sequence scrambling is a charge dependent phenomenon, which affects CAD of doubly charged peptides far more than their singly charged counterparts.
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Affiliation(s)
- Junmei Zhang
- Protein Chemistry Technology Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, USA
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Zee BM, Young NL, Garcia BA. Quantitative proteomic approaches to studying histone modifications. CURRENT CHEMICAL GENOMICS 2011; 5:106-14. [PMID: 21966350 PMCID: PMC3178935 DOI: 10.2174/1875397301005010106] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 03/26/2011] [Accepted: 04/25/2011] [Indexed: 11/22/2022]
Abstract
Histone post-translational modifications (PTMs) positively and negatively regulate gene expression, and are consequently a vital influence on the genomic profile of all eukaryotic species. The study of histone PTMs using classical methods in molecular biology, such as immunofluorescence and Western blotting, is challenging given the technical issues of the approaches, and chemical diversity and combinatorial patterns of the modifications. In light of these many technical limitations, mass spectrometry (MS) is emerging as the most unbiased and rigorous experimental platform to identify and quantify histone PTMs in a high-throughput manner. This review covers the latest developments in mass spectrometry for the analysis of histone PTMs, with the hope of inspiring the continued integration of proteomic, genomic and epigenetic research.
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Affiliation(s)
- Barry M Zee
- 415 Schultz Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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