American Chemical Society
ac061515x_si_002.xls (365 kB)

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

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posted on 2007-02-15, 00:00 authored by Moshe Havilio, Assaf Wool
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.