As with all shotgun proteomics experiments, global quantitative post-translational modification (PTM) proteomics relies heavily on appropriate bioinformatics analyses. The relevant bioinformatics methods associated with global quantitative post-translational modification proteomics are confident identification and validation of thousands of PTM peptides from MS/MS spectra, determination of stoichiometry of PTM peptides, localization of PTM sites, and measurement of the ratio of PTM peptides. Each one of these steps is of equal importance. That is if anyone of these steps is inaccurate or of low confidence, the entire quantitative analysis is equally inaccurate and of low confidence.
Identification of PTM peptide sequences and measurement of PTM peptides leverages the accuracy of global quantitative proteomics (i.e. SEQUEST, ProLuCID, DTASelect, Census, AScore, and Luciphor). When the appropriate filtering methods are used, these two steps are already of high confidence. The remaining essential steps of PTM peptide validation, determination of stoichiometry of PTM peptides and site localization have been addressed by the introduction of AScore or Luciphor.