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Gas-Phase Fragmentation of ADP-Ribosylated Peptides: Arginine-Specific Side-Chain Losses and Their Implication in Database Searches

  • Peter M. Gehrig*
    Peter M. Gehrig
    Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
    *Mailing address: Functional Genomics Center Zurich, Winterthurerstrasse 190, Zurich, Switzerland. Telephone number: +41 44 635 39 08. Fax number: +41 44 635 39 22. E-mail address: [email protected]
  • Kathrin Nowak
    Kathrin Nowak
    Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
    Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
  • Christian Panse
    Christian Panse
    Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
    SIB Swiss Institute of Bioinformatics, Quartier Sorge−Batiment Amphipole 1015, Lausanne, Switzerland
  • Mario Leutert
    Mario Leutert
    Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
  • Jonas Grossmann
    Jonas Grossmann
    Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
    SIB Swiss Institute of Bioinformatics, Quartier Sorge−Batiment Amphipole 1015, Lausanne, Switzerland
  • Ralph Schlapbach
    Ralph Schlapbach
    Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
  • , and 
  • Michael O. Hottiger
    Michael O. Hottiger
    Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
Cite this: J. Am. Soc. Mass Spectrom. 2021, 32, 1, 157–168
Publication Date (Web):November 3, 2020
https://doi.org/10.1021/jasms.0c00040
Copyright © 2020 American Society for Mass Spectrometry. Published by American Chemical Society. All rights reserved.

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    Abstract

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    ADP-ribosylation is a reversible post-translational modification of proteins that has been linked to many biological processes. The identification of ADP-ribosylated proteins and particularly of their acceptor amino acids remains a major challenge. The attachment sites of the modification are difficult to localize by mass spectrometry (MS) because of the labile nature of the linkage and the complex fragmentation pattern of the ADP-ribose in MS/MS experiments. In this study we performed a comprehensive analysis of higher-energy collisional dissociation (HCD) spectra acquired from ADP-ribosylated peptides which were modified on arginine, serine, glutamic acid, aspartic acid, tyrosine, or lysine residues. In addition to the fragmentation of the peptide backbone, various cleavages of the ADP-ribosylated amino acid side chains were investigated. We focused on gas-phase fragmentations that were specific either to ADP-ribosylated arginine or to ADP-ribosylated serine and other O-linked ADP-ribosylations. The O-glycosidic linkage between ADP-ribose and serine, glutamic acid, or aspartic acid was the major cleavage site, making localization of these modification sites difficult. In contrast, the bond between ADP-ribose and arginine was relatively stable. The main cleavage site was the inner bond of the guanidine group, which resulted in the formation of ADP-ribosylated carbodiimide and of ornithine in place of modified arginine. Taking peptide fragment ions resulting from this specific cleavage into account, a considerably larger number of peptides containing ADP-ribosylated arginine were identified in database searches. Furthermore, the presence of diagnostic ions and of losses of fragments from peptide ions allowed us, in most cases, to distinguish between ADP-ribosylated arginine and serine residues.

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    Cited By

    This article is cited by 18 publications.

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