Abstract
Protein identification via mass spectrometry (MS) relies primarily on protein sequence databases. Identification resulting from a sequence database search in the tandem mass spectrometry (MS/MS) experiments for the digested peptides is derived from an algorithm based on statistical confidence, and therefore, it often pro- ides false-positive identifications. Although one can apply high-resolution MS such as Fourier-transform mass spectrometer (FT-MS) to obtain results with high confidence, the instrumentation is expensive and the results are still probability based. Therefore, we introduced data-dependent triple stage mass spectrometry (MS3) into our well-established liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis of linear ion trap MS to achieve evidence-based protein identification. Peptide sequencing by MS3 analysis can provide a direct evidence for a sequence elucidated by MS/MS data and help determine whether the search results are correct.
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