title: Mass spectrometrists should search only for peptides they care about.
abstract: Analysis pipelines that assign peptides to shotgun proteomics mass spectra often discard identified spectra deemed irrelevant to the scientific hypothesis being tested. To improve statistical power, I propose that researchers remove irrelevant peptides from the database prior to searching rather than assigning these peptides to spectra and then discarding the matches.
authors.affiliation: Department of Genome Sciences and the Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA.
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
mesh_terms: D006801:Humans; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis; D010961:Plasmodium / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides