Filtering of MS/MS data for peptide identification

The availability of fast, relatively inexpensive data analysis through tandem mass spectrometry has ushered in an era of “shotgun proteomics.” Biologists can easily fragment large numbers of samples, and obtain extremely accurate measurements of fragment mass; from this, it is possible to work backwards to identify parent peptides and proteins. To obtain accurate identifications, however, it is necessary to filter the raw data, separating noise from primary parent ions. In this paper, we utilize a new technique based on orthogonal polynomials to filter raw MS/MS data without the need for manual tuning. The effectiveness of the approach is shown through dramatic increases in the accuracy of identifications with a de novo method, with results rivaling those of the best available database matching methods.