Preview: A Program for Surveying Shotgun Proteomics Tandem Mass Spectrometry Data
Preview analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications to facilitate parameter selection.
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Preview: A Program for Surveying Shotgun Proteomics Tandem Mass Spectrometry Data
Anal Chem. 2011 Jul 1;83(13):5259-67. doi: 10.1021/ac200609a. Epub 2011 Jun 13.
Yong J Kil, Christopher Becker, Wendy Sandoval, David Goldberg, Marshall Bern
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%.
