A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

ABSTRACT: Less than half of all MS/MS spectra acquired in shotgun proteomics typically result in a confident peptide match. Here we present an ultra-tolerant Sequest database search that allowed peptide matching even with modifications of unknown masses up to ±500 Da. From an HEK293 cell proteome-wide dataset (9,513 proteins and 396,736 peptides), a ±500-Da search matched an additional 184,000 modified peptides. These were linked to both biological and chemical modifications representing 523 distinct mass bins including phosphorylation, glycosylation, and methylation. We attempted to localize all unknown modification masses to specific regions within a peptide, and known modifications were accurately assigned to the correct amino acids with frequencies often >90%. These data demonstrate that a large fraction of previously unassignable spectra are assignable to peptide sequences with modifications.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Brain, Kidney

SUBMITTER: Joel Chick  

LAB HEAD: Steven P Gygi

PROVIDER: PXD001468 | Pride | 2015-06-03

REPOSITORIES: Pride