title: ScanRanker: Quality assessment of tandem mass spectra via sequence tagging.
abstract: In shotgun proteomics, protein identification by tandem mass spectrometry relies on bioinformatics tools. Despite recent improvements in identification algorithms, a significant number of high quality spectra remain unidentified for various reasons. Here we present ScanRanker, an open-source tool that evaluates the quality of tandem mass spectra via sequence tagging with reliable performance in data from different instruments. The superior performance of ScanRanker enables it not only to find unassigned high quality spectra that evade identification through database search but also to select spectra for de novo sequencing and cross-linking analysis. In addition, we demonstrate that the distribution of ScanRanker scores predicts the richness of identifiable spectra among multiple LC-MS/MS runs in an experiment, and ScanRanker scores assist the process of peptide assignment validation to increase confident spectrum identifications. The source code and executable versions of ScanRanker are available from http://fenchurch.mc.vanderbilt.edu.
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-8340, USA.
authors.forename: Ze-Qiang
authors.initials: ZQ
authors.lastname: Ma
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Chambers
authors.forename: Amy-Joan L
authors.initials: AJ
authors.lastname: Ham
authors.forename: Kristin L
authors.initials: KL
authors.lastname: Cheek
authors.forename: Corbin W
authors.initials: CW
authors.lastname: Whitwell
authors.forename: Hans-Rudolf
authors.initials: HR
authors.lastname: Aerni
authors.forename: Birgit
authors.initials: B
authors.lastname: Schilling
authors.forename: Aaron W
authors.initials: AW
authors.lastname: Miller
authors.forename: Richard M
authors.initials: RM
authors.lastname: Caprioli
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
mesh_terms: D000465:Algorithms; D000818:Animals; D002853:Chromatography, Liquid; D019295:Computational Biology; D030562:Databases, Protein; D006801:Humans; D010446:Peptide Fragments / Q000032:analysis* / Q000737:chemistry; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012107:Research Design; D020539:Sequence Analysis, Protein; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010446:Peptide Fragments; D011506:Proteins