PXD040898

PXD040898 is an original dataset announced via ProteomeXchange.

Title	A combined gas phase separation strategy for ADP-ribosylated peptides
Description	ADP-ribosylation (ADPr) is a posttranslational modification that is best studied using mass spectrometry. Method developments that are permissive to low inputs or baseline levels of protein ribosylation represent the next frontier in the field. High-field asymmetric waveform ion mobility spectrometry (FAIMS) reduces peptide complexity in gas phase, providing a means to achieve maximal ADPr peptide sequencing depth. We therefore investigated the extent to which FAIMS with or without traditional gas-phase fractionation/separation (GPS) can increase the number of ADPr peptides. We examined ADPr peptides enriched from mouse spleens. We gleaned additional insight by also reporting findings from the corresponding non-ADPr peptide contaminants, and the peptide inputs for ADPr peptide enrichment. At increasingly higher compensation voltages, ADPr peptides were more stable whereas the non-ADPr peptides were filtered out. A combination of 3 GPS survey scans, each with 8 compensation voltages resulted in 790 high-confidence ADPr peptides, compared to 90 with GPS alone. A simplified acquisition strategy requiring only two injections corresponding to two MS1 scan ranges coupled to optimized compensation voltage settings, provided 402 ADPr peptides corresponding to 234 ADPr proteins. We conclude that our combined gas phase separation strategy is a valuable addition to any ADP-ribosylome workflow.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:04:56.139.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD040898
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sasha Singh
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	adenosine diphosphoribosyl (ADP-ribosyl) modified residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-15 12:47:53	ID requested
1	2023-08-30 16:04:23	announced
⏵ 2	2023-11-14 09:05:04	announced	2023-11-14: Updated project metadata.

Kasai T, Kuraoka S, Higashi H, Delanghe B, Aikawa M, Singh SA, A Combined Gas-Phase Separation Strategy for ADP-ribosylated Peptides. J Am Soc Mass Spectrom, 34(10):2136-2145(2023) [pubmed]

10.6019/PXD040898;

submitter keyword: mono-ADP-ribose,Gas-phase segmentation, ribosylation, high field asymmetric waveform ion mobility spectrometry, gas-phase fragmentation

Masanori Aikawa
contact affiliation	Brigham and Women's Hospital
contact email	maikawa@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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/08/PXD040898

PRIDE project URI

• PRIDE
  1. PXD040898
     1. Label: PRIDE project
     2. Name: A combined gas phase separation strategy for ADP-ribosylated peptides