Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries

A widespread proteomics procedure for characterizing a complex mixture of proteins combines tandem mass spectrometry and database search software to yield mass spectra with identified peptide sequences. The same peptides are often detected in multiple experiments, and once they have been identified, the respective spectra can be used for future identifications. We present a method for collecting previously identified tandem mass spectra into a reference library that is used to identify new spectra. Query spectra are compared to references in the library to find the ones that are most similar. A dot product metric is used to measure the degree of similarity. With our largest library, the search of a query set finds 91% of the spectrum identifications and 93.7% of the protein identifications that could be made with a SEQUEST database search. A second experiment demonstrates that queries acquired on an LCQ ion trap mass spectrometer can be identified with a library of references acquired on an LTQ ion trap mass spectrometer. The dot product similarity score provides good separation of correct and incorrect identifications.