PXD059650

PXD059650 is an original dataset announced via ProteomeXchange.

Title	Searching for Sulfotyrosines (sY) in a H A( pY ) STACK
Description	Protein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is near-isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The degree to which tyrosine sulfation (sY) is misidentified as phosphorylation (pY) is thus an unresolved concern. This study explores the extent of sY misidentification within the human phosphoproteome by distinguishing between sulfation and phosphorylation based on their mass difference. Using Gaussian mixture models (GMMs), we screened ~45M peptide-spectrum matches (PSMs) from the PeptideAtlas Human Phosphoproteome build for peptidoforms with mass error shifts indicative of sulfation. This analysis pinpointed 104 candidate sulfated peptidoforms, backed-up by Gene Ontology (GO) terms and custom terms linked to sulfation. False positive filtering by manual annotation resulted in 31 convincing peptidoforms spanning 7 known and 7 novel sY sites. Y47 in Calumenin was particularly intriguing since mass error shifts, acidic motif conservation, and MS2 neutral loss patterns characteristic of sulfation, but not phosphorylation, provided strong evidence that this site can only be sulfated. Overall, although misidentification of sulfation in phosphoproteomics datasets derived from cell and tissue intracellular extracts can occur, it appears relatively rare and should not be considered a confounding factor for high-quality phosphoproteomics studies. Protein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is near-isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The degree to which tyrosine sulfation (sY) is misidentified as phosphorylation (pY) is thus an unresolved concern. This study explores the extent of sY misidentification within the human phosphoproteome by distinguishing between sulfation and phosphorylation based on their mass difference. Using Gaussian mixture models (GMMs), we screened ~45M peptide-spectrum matches (PSMs) from the PeptideAtlas Human Phosphoproteome build for peptidoforms with mass error shifts indicative of sulfation. This analysis pinpointed 104 candidate sulfated peptidoforms, backed-up by Gene Ontology (GO) terms and custom terms linked to sulfation. False positive filtering by manual annotation resulted in 31 convincing peptidoforms spanning 7 known and 7 novel sY sites. Y47 in Calumenin was particularly intriguing since mass error shifts, acidic motif conservation, and MS2 neutral loss patterns characteristic of sulfation, but not phosphorylation, provided strong evidence that this site can only be sulfated. Overall, although misidentification of sulfation in phosphoproteomics datasets derived from cell and tissue intracellular extracts can occur, it appears relatively rare and should not be considered a confounding factor for high-quality phosphoproteomics studies.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_06:26:32.450.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD059650
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sally Oswald
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	sulfated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-10 12:29:47	ID requested
⏵ 1	2025-05-07 06:26:33	announced

Tzvetkov J, Eyers CE, Eyers PA, Ramsbottom KA, Oswald SO, Harris JA, Sun Z, Deutsch EW, Jones AR, Searching for Sulfotyrosines (sY) in a HA(pY)STACK. J Proteome Res, 24(3):1250-1264(2025) [pubmed]

10.1021/acs.jproteome.4c00907;

10.6019/PXD059650;

submitter keyword: tyrosine sulfation, proteomics, misidentification, large scale meta - analysis, phosphorylation,Mass spectrometry

Prof. Claire Eyers
contact affiliation	Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
contact email	ceyers@liverpool.ac.uk
lab head
Sally Oswald
contact affiliation	University of Liverpool
contact email	sallyo@liverpool.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD059650
     1. Label: PRIDE project
     2. Name: Searching for Sulfotyrosines (sY) in a H A( pY ) STACK