Method for protein identification using mass spectrometry data

The present teachings describe methods for matching a query peptide to a database of known peptides based on a mass analysis approach. The methods described herein facilitate rapid, sensitive, and selective identification of an unknown query peptide and provide the ability to develop applications which perform substantially automated high throughput protein identification. The methods described herein also allow for mass spectrometry data for a query peptide to be categorized and weighted according to its quality. Furthermore, the methods described herein provide robust identification of modified query proteins by either anticipating modifications or adjusting for modified peptide masses.