PXD017013

PXD017013 is an original dataset announced via ProteomeXchange.

Title	Gas-phase Fragmentation of ADP-Ribosylated Peptides: Arginine-Specific Side-Chain Losses and their Implication in Database Searches
Description	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 of their acceptor amino acids remains a significant challenge. The attachment sites of the modification are difficult to study by mass spectrometry (MS) because of its labile nature and its complex fragmentation pattern in MS/MS experiments. In this study we performed a detailed 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. In addition to the fragmentation of the peptide backbone, various cleavages of bonds within the ADP-ribose, and between the modification and the amino acid residue, have to be considered. We focused on gas-phase fragmentations that are 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 is the major cleavage site, making localization of these modification sites difficult. In contrast, the bond between ADP-ribose and arginine is relatively stable. The main cleavage site is the inner bond of the guanidine which results in the formation of ADP-ribosylated carbodiimide and of ornithine in place of modified arginine. Taking this specific cleavage into account, a considerably larger number of peptides containing ADP-ribosylated arginine were identified in database searches, and their modification sites were assigned with increased confidence.
HostingRepository	PRIDE
AnnounceDate	2021-05-19
AnnouncementXML	Submission_2021-05-19_06:52:57.310.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Peter Gehrig
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	adenosine diphosphoribosyl (ADP-ribosyl) modified residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-08 06:07:27	ID requested
⏵ 1	2021-05-19 06:52:58	announced

Gehrig PM, Nowak K, Panse C, Leutert M, Grossmann J, Schlapbach R, Hottiger MO, Gas-Phase Fragmentation of ADP-Ribosylated Peptides: Arginine-Specific Side-Chain Losses and Their Implication in Database Searches. J Am Soc Mass Spectrom, 32(1):157-168(2021) [pubmed]

Leutert M, Menzel S, Braren R, Rissiek B, Hopp AK, Nowak K, Bisceglie L, Gehrig P, Li H, Zolkiewska A, Koch-Nolte F, Hottiger MO, Proteomic Characterization of the Heart and Skeletal Muscle Reveals Widespread Arginine ADP-Ribosylation by the ARTC1 Ectoenzyme. Cell Rep, 24(7):1916-1929.e5(2018) [pubmed]

curator keyword: Technical

submitter keyword: Post-translational modification, ADP-ribosylation, arginine, neutral loss, marker ion, mass spectrometry, Orbitrap Fusion

Michael Hottiger
contact affiliation	Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
contact email	michael.hottiger@dmmd.uzh.ch
lab head
Peter Gehrig
contact affiliation	Functional Genomics Center Zurich University and ETH Zurich Winterthurerstrasse 190 8057 Zurich
contact email	peter.gehrig@fgcz.uzh.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017013
     1. Label: PRIDE project
     2. Name: Gas-phase Fragmentation of ADP-Ribosylated Peptides: Arginine-Specific Side-Chain Losses and their Implication in Database Searches