ScanRanker: Quality assessment of tandem mass spectra via sequence tagging.

Ma ZQ, Chambers MC, Ham AJ, Cheek KL, Whitwell CW, Aerni HR, Schilling B, Miller AW, Caprioli RM, Tabb DL
J Proteome Res. 2011 10 (7): 2896-904

PMID: 21520941 · PMCID: PMC3128668 · DOI:10.1021/pr200118r

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

MeSH Terms (12)

Algorithms Animals Chromatography, Liquid Computational Biology Databases, Protein Humans Peptide Fragments Proteins Proteomics Research Design Sequence Analysis, Protein Tandem Mass Spectrometry

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