PXD026448

PXD026448 is an original dataset announced via ProteomeXchange.

Title	FAIMS enhances the detection of PTM crosstalk sites
Description	Protein post-translational modification (PTMs) enable cells to rapidly change in response to biological stimuli. With over 400 PTMs, understanding these control mechanisms is complex. To date, efforts have focused on investigating the effect of single PTMs on protein function. Yet, many proteins contain multiple PTMs. Moreover, one PTM can alter the prevalence of another; a phenomenon termed PTM crosstalk. Understanding PTM crosstalk is critical; however, its detection is challenging since PTMs occur sub-stoichiometrically. In this work, we developed an enrichment-free, label-free proteomics method that utilized high field asymmetric ion mobility spectrometry (FAIMS) to enhance the detection of PTM crosstalk. We showed that by searching for multiple combinations of dynamic PTMs on peptide sequences, a large increase in identifications of candidate PTM crosstalk sites was observed compared with standard LC-MS/MS. Additionally, by cycling through FAIMS compensation voltages within a single LC-FAIMS-MS/MS run, we showed that our LC-FAIMS-MS/MS workflow could increase multi-PTM containing peptide identifications without additional increases in run times. With more novel candidate crosstalk sites identified, we envisage LC-FAIMS-MS/MS to play an important role in expanding the repertoire of multi-PTM identifications. Moreover, it is only by detecting PTM crosstalk, that we can ‘see’ the full picture of how proteins are regulated.
HostingRepository	PRIDE
AnnounceDate	2025-03-11
AnnouncementXML	Submission_2025-03-11_07:31:03.071.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD026448
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Aneika Leney
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; N-acetylaminoglucosylated residue; ubiquitination signature dipeptidyl lysine; phosphorylated residue; acetylated residue; monohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-03 02:43:22	ID requested
⏵ 1	2025-03-11 07:31:03	announced

Adoni KR, Cunningham DL, Heath JK, Leney AC, FAIMS Enhances the Detection of PTM Crosstalk Sites. J Proteome Res, 21(4):930-939(2022) [pubmed]

10.1021/acs.jproteome.1c00721;

submitter keyword: FAIMS,LC-MS, post-translational modifications, interplay, crosstalk

Aneika Leney
contact affiliation	School of Biosciences, University of Birmingham, UK
contact email	a.leney@bham.ac.uk
lab head
Aneika Leney
contact affiliation	University of Birmingham
contact email	a.leney@bham.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026448
     1. Label: PRIDE project
     2. Name: FAIMS enhances the detection of PTM crosstalk sites