Large-Scale Unrestricted Identification of Post-Translation Modifications Using Tandem Mass Spectrometry

TwinPeaks, a close variant of the SEQUEST protein
identification algorithm, is capable of unrestricted, large-scale, identification of post-translation modifications
(PTMs). TwinPeaks is applied on a sample of 100441
tandem mass spectra from the HUPO Plasma Proteome
Project data set, with full non-redundant human as a
reference protein database. With a 3.5% error rate,
TwinPeaks identifies a collection of 539 spectra that were
not identified by the usual PTM-restricted identification
algorithm. At this error rate, TwinPeaks increases the rate
of spectra identifications by at least 17.6%, making
unrestricted PTM identification an integral part of proteomics.