Figure 1

Shotgun proteomics workflow and analysis pipeline used for PTM identifications. (A) In the dataset analysed herein, cardiac tissue was homogenized, proteins were extracted from the tissue and enzymatically digested to peptides by trypsin. The peptide mixture was then measured on a high-resolution tandem mass spectrometer from which MS/MS spectra were obtained. These MS/MS spectra were then searched with the Comet-PTM search engine against a human protein database and the results were processed with SHIFTS for PTM peak detection and FDR control. Detected PTM peaks were subsequently annotated by the tools PTM-sticker and PTM-Shepherd. (B) Cumulative frequency distribution of Δ masses obtained by the Comet-PTM and SHIFTS analysis of human heart proteome dataset. In the figure, highlighted peaks represent different PTMs identified based on their Δ Mass in the range of − 55 to 200 Dalton. Phosphorylation of a peptide is for instance identified in the tandem mass spectrum as a mass shift of 79.966 Dalton and methylation is identified as mass shift of 14.015.