title: Preview: a program for surveying shotgun proteomics tandem mass spectrometry data.
abstract: Database search programs for peptide identification by tandem mass spectrometry ask their users to set various parameters, including precursor and fragment mass tolerances, digestion specificity, and allowed types of modifications. Even proteomics experts with detailed knowledge of their samples may find it difficult to make these choices without significant investigation, and poor choices can lead to missed identifications and misleading results. Here we describe a program called Preview that analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications, thereby facilitating parameter selection. Moreover, Preview optionally recalibrates mass over charge measurements, leading to further improvement in identification results. In a study of Bruton's tyrosine kinase, we find that the use of Preview improved the number of confidently identified mass spectra and phosphorylation sites by about 50%.
authors: Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304, USA.
authors: Yong J
authors: YJ
authors: Kil
authors: Christopher
authors: C
authors: Becker
authors: Wendy
authors: W
authors: Sandoval
authors: David
authors: D
authors: Goldberg
authors: Marshall
authors: M
authors: Bern
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