title: A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics.
abstract: Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, because this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referenced as Statistical Tools for AMT Tag Confidence (STAC). STAC additionally provides a uniqueness probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download, as both a command line and a Windows graphical application.
authors.affiliation: Department of Statistics, Texas A&M University, College Station, Texas 77840, United States.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Stanley
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.forename: Gordon W
authors.initials: GW
authors.lastname: Slysz
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Monroe
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Purvine
authors.forename: Yuliya V
authors.initials: YV
authors.lastname: Karpievitch
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Anderson
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Alan R
authors.initials: AR
authors.lastname: Dabney
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000592:standards / Q000706:statistics & numerical data*; D030562:Databases, Protein; D015233:Models, Statistical; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011336:Probability; D040901:Proteomics / Q000379:methods / Q000706:statistics & numerical data*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000592:standards / Q000706:statistics & numerical data*
chemical_list: D010455:Peptides