MODplus: Robust and Unrestrictive Identification of Post-Translational Modifications Using Mass Spectrometry

Post-translational
modifications regulate various cellular processes
and are of great biological interest. Unrestrictive searches of mass
spectrometry data enable the detection of any type of modification.
Here we propose MODplus, which makes practical unrestrictive searches
possible by allowing (1) hundreds of modifications, (2) multiple modifications
per peptide, (3) the whole proteome database, and (4) any tolerant
values in search parameters. The utility of MODplus was demonstrated
in large human data sets of HEK293 cells and TMT-labeled phosphorylation
enrichment. Notably, MODplus supports identifying different modification
types at multiple sites and reports real chemical and biological modifications,
as it has been very labor intensive to link unrestrictive search results
to real modifications. We also confirmed the presence of Missing
Precursor (MP) spectra that were not identifiable
using targeted precursor masses. The MP spectra mostly resulted in
identifications of wrong modifications and negatively affected the
overall performance, often by as much as 10%. MODplus can rapidly
recognize MP spectra and correct their identifications, resulting
in increased identification rate up to 70% in the HEK293 data set
as well as improved reliability.