Tandem Mass Spectrum Identification via Cascaded Search

• Activity Number: 9
• Type: Invited
• Date/Time: Sunday, August 9, 2015 : 2:00 PM to 3:50 PM
• Sponsor: WNAR
• Author(s): William Stafford Noble* and Attila Kertesz-Farkas and Uri Keich
• Companies: University of Washington and University of Washington and University of Sydney
• Keywords: multiple testing ; mass spectrometry

Abstract

Many protocols for the analysis of shotgun proteomics mass spectra attempt to mitigate the multiple testing problem by controlling the hypothesis space in various ways: only considering peptides resulting from enzymatic cleavages, ignoring possible post-translational modifications, etc. However, these strategies cannot identify spectra generated by rarer types of peptides. We describe a statistical testing framework, cascaded search, to solve this problem. The method requires that the user specify a statistical confidence threshold as well as a series of peptide databases. For instance, such a cascade of databases could include fully tryptic, semi-tryptic and non-enzymatic peptides, or peptides with increasing numbers of modifications. Cascaded search then gradually expands the list of candidate peptides from more likely peptides toward rare peptides, sequestering at each stage any spectrum that is identified with a specified statistical confidence. We demonstrate that the proposed approach yields improved statistical power relative to commonly used protocols.