Searching for Sulfotyrosines (sY) in a HA(pY)STACK

Protein sulfation can be crucial in regulating protein–protein
interactions but remains largely underexplored. Sulfation is nearly
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 ∼45 M 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 provided strong
evidence that this site is sulfated rather than phosphorylated. Overall,
although misidentification of sulfation in phosphoproteomics data
sets derived from cell and tissue intracellular extracts can occur,
it appears relatively rare and should not be considered a substantive
confounding factor in high-quality phosphoproteomics data sets.