PXD055586-1

PXD055586 is an original dataset announced via ProteomeXchange.

Title	In-source CID improves HCD-dependent fragmentation of ADP-ribosyl peptides
Description	ADP-ribosylation is a posttranslational modification whose HCD products are dominated by complete or partial modification losses, complicating peptide sequencing and acceptor site localization efforts. We tested whether in-source CID performed on a quadrupole Orbitrap could convert ADPr to the smaller phosphoribose-H2O derivative to facilitate HCD-dependent peptide sequencing. Human macrophage like cell line THP-1-derived ADP-ribosyl (ADPr) peptides were analyzed on a quadrupole Orbitrap. We monitored the interconversion of ADPr (+541.061 Da) to phosphoribosyl-H2O (+193.997 Da) peptides while varying the source and high-field asymmetric waveform ion mobility mass spectrometry (FAIMS) compensation voltages. Xcorr and ptmRS were used to evaluate peptide sequencing and acceptor site confidence, respectively. In-source CID-HCD-derived phosphoribosyl-H2O acceptor sites were compared to those determined by EThcD, performed on a quadrupole ion trap Orbitrap. Interconversion of ADPr peptides to their phosphoribosyl-H2O derivatives increased with increasing source voltage (up to 50V), as judged by monitoring the corresponding modification loss ([adenosine monophosphate/AMP]+) and the number of identified phosphoribosyl-H2O peptide identifications. The average Xcorr increased from 1.36 (ADPr) to 2.26 (phosphoribosyl-H2O), similar to that achieved with EThcD for ADPr peptides (2.29). The number of high-confidence acceptor sites (>95%) also increased, from 31% (ADPr) to 70% (phosphoribosyl-H2O), which was comparable to EThcD (70%). In-source CID converts ADP-ribosyl to phosphoribosyl-H2O peptides that are more amenable to HCD-dependent peptide sequencing, providing an alternative method for acceptor site determination when ETD-based methods are not available.
HostingRepository	PRIDE
AnnounceDate	2024-12-05
AnnouncementXML	Submission_2024-12-05_10:14:35.050.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD055586
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sasha Singh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	adenosine diphosphoribosyl (ADP-ribosyl) modified residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-05 06:20:08	ID requested
⏵ 1	2024-12-05 10:14:35	announced

Kasai T, Nakamura Y, Aikawa M, Singh SA, In-Source Collision-Induced Dissociation (CID) Improves Higher-Energy Collisional Dissociation (HCD)-Dependent Fragmentation of ADP-Ribosyl Peptides. Rapid Commun Mass Spectrom, 39(4):e9961(2025) [pubmed]

10.6019/PXD055586;

10.1002/rcm.9961;

submitter keyword: SID, proteomics, HCD, Exploris480,ADP-ribosylation

Sasha A.
contact affiliation	Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham Women's Hospital, Harvard Medical School, Boston, MA, United States
contact email	sasingh@bwh.harvard.edu
lab head
Sasha Singh
contact affiliation	Brigham and Women's Hospital, Harvard Medical School
contact email	sasingh@bwh.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD055586
     1. Label: PRIDE project
     2. Name: In-source CID improves HCD-dependent fragmentation of ADP-ribosyl peptides