Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS: PTM-SWATH-MS Gold Standard data set

The PTM-SWATH MS Gold Standard data set consists of a previously published (Soste et al., 2014, PMID:25194849) set of 579 unpurified, synthetic, heavy-isotope labeled phosphopeptides (Thermo Scientific Biopolymers). These phosphopeptides represent biologically relevant sequences from S. cerevisiae proteins, which have been found altered in their phosphorylation status under various conditions. The complete peptide set contains a mixture of singly and doubly phosphorylated sequences with in average more than 3 modifiable residues per peptide (serines, threonines or tyrosins, often in close proximity to each other). All peptides were mixed with equal volumes (concentrations are unknown due to the unpurified status of the peptides) and the resulting peptide mix was either analyzed directly in DDA mode for assay library generation or spiked into a human cell line background proteome in a 13-step dilution series and analyzed in SWATH mode for the generation of the SWATH Gold Standard data set.