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Technological Innovation and Resources

ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides

Daniel Paul Zolg, View ORCID ProfileMathias Wilhelm, Tobias Schmidt, Guillaume Médard, Johannes Zerweck, Tobias Knaute, Holger Wenschuh, Ulf Reimer, Karsten Schnatbaum and Bernhard Kuster  Correspondence email
Molecular & Cellular Proteomics September 1, 2018, First published on May 29, 2018, 17 (9) 1850-1863; https://doi.org/10.1074/mcp.TIR118.000783
Daniel Paul Zolg
From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
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Mathias Wilhelm
From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
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  • ORCID record for Mathias Wilhelm
Tobias Schmidt
From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
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Guillaume Médard
From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
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Johannes Zerweck
§JPT Peptide Technologies GmbH, Berlin, Germany;
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Tobias Knaute
§JPT Peptide Technologies GmbH, Berlin, Germany;
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Holger Wenschuh
§JPT Peptide Technologies GmbH, Berlin, Germany;
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Ulf Reimer
From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
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Karsten Schnatbaum
§JPT Peptide Technologies GmbH, Berlin, Germany;
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Bernhard Kuster
From the ‡Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; ¶Center for Integrated Protein Science Munich, Freising, Germany; ‖Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
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  • For correspondence: kuster@tum.de
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Abstract

The analysis of the post-translational modification (PTM) state of proteins using mass spectrometry-based bottom-up proteomic workflows has evolved into a powerful tool for the study of cellular regulatory events that are not directly encoded at the genome level. Besides frequently detected modifications such as phosphorylation, acetylation and ubiquitination, many low abundant or less frequently detected PTMs are known or postulated to serve important regulatory functions. To more broadly understand the LC-MS/MS characteristics of PTMs, we synthesized and analyzed ∼5,000 peptides representing 21 different naturally occurring modifications of lysine, arginine, proline and tyrosine side chains and their unmodified counterparts. The analysis identified changes in retention times, shifts of precursor charge states and differences in search engine scores between modifications. PTM-dependent changes in the fragmentation behavior were evaluated using eleven different fragmentation modes or collision energies. We also systematically investigated the formation of diagnostic ions or neutral losses for all PTMs, confirming 10 known and identifying 5 novel diagnostic ions for lysine modifications. To demonstrate the value of including diagnostic ions in database searching, we reprocessed a public data set of lysine crotonylation and showed that considering the diagnostic ions increases confidence in the identification of the modified peptides. To our knowledge, this constitutes the first broad and systematic analysis of the LC-MS/MS properties of common and rare PTMs using synthetic peptides, leading to direct applicable utility for bottom-up proteomic experiments.

  • Peptide Synthesis
  • Post-translational modifications
  • Peptides
  • Phosphorylation
  • Acetylation
  • Bioinformatics
  • Tandem Mass Spectrometry
  • Methylation
  • diagnostic ion
  • immonium ion
  • neutral loss
  • peptide fragmentation
  • ProteomeTools

Footnotes

  • Author Contributions: K.S., U.R, D.P.Z., M.W., and B.K. conceived the study. D.P.Z, K.S., and T.K. selected the peptide sequences. J.Z. synthesized the peptides. D.P.Z., T.S., and M.W. generated the data. D.P.Z., M.W., and G.M. analyzed the data. D.P.Z., M.W., K.S., H.W., U.R., and B.K. discussed the results. D.P.Z. and B.K. wrote the manuscript.

  • ↵* This work was in part funded by the German Federal Ministry of Education and Research (BMBF; grant no. 031L0008A) in the context of the ProteomeTools project (www.proteometools.org). M.W. and B.K. are founders and shareholders of OmicScouts GmbH, which operates in the field of proteomics. They have no operational role in the company. J.Z., T.K., K.S., and U.R. are employees of JPT Peptide Technologies GmbH. Parts of the synthetic peptides used in the study are commercialized by JPT.

  • ↵Embedded Image This article contains supplemental material.

  • Received April 13, 2018.
  • Revision received May 21, 2018.
  • © 2018 Zolg et al.

Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc.

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ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides
Daniel Paul Zolg, Mathias Wilhelm, Tobias Schmidt, Guillaume Médard, Johannes Zerweck, Tobias Knaute, Holger Wenschuh, Ulf Reimer, Karsten Schnatbaum, Bernhard Kuster
Molecular & Cellular Proteomics September 1, 2018, First published on May 29, 2018, 17 (9) 1850-1863; DOI: 10.1074/mcp.TIR118.000783

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ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides
Daniel Paul Zolg, Mathias Wilhelm, Tobias Schmidt, Guillaume Médard, Johannes Zerweck, Tobias Knaute, Holger Wenschuh, Ulf Reimer, Karsten Schnatbaum, Bernhard Kuster
Molecular & Cellular Proteomics September 1, 2018, First published on May 29, 2018, 17 (9) 1850-1863; DOI: 10.1074/mcp.TIR118.000783
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Molecular & Cellular Proteomics: 17 (9)
Molecular & Cellular Proteomics
Vol. 17, Issue 9
1 Sep 2018
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