Unbiased statistical analysis for multi-stage proteomic search strategies.
"Multi-stage" search strategies have become widely accepted for peptide identification and are implemented in a number of available software packages. We describe limitations of these strategies for validation and decoy-based statistical analyses and demonstrate these limitations using a set of control sample spectra. We propose a solution that corrects the statistical deficiencies and describe its implementation using the open-source software X!Tandem.
Everett
Logan J
LJ
University of Pennsylvania, Department of Pathology and Laboratory Medicine, 613A Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA.
Bierl
Charlene
C
Master
Stephen R
SR
D002853:Chromatography, Liquid; D040901:Proteomics; D012984:Software; D053719:Tandem Mass Spectrometry