ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging

peer-reviewed · Journal of Proteome Research · 2011

peer-reviewed · Journal of Proteome Research · 2011. Ze-Qiang Ma et al. In shotgun proteomics, protein identification by tandem mass spectrometry relies on bioinformatics tools…
Date 2011-07-01
Type peer-reviewed
Venue Journal of Proteome Research
Publisher American Chemical Society (ACS)
Contribution adjacent
DOI 10.1021/pr200118r
Citations (OpenAlex) 38
Venue 2-year citedness 3.83

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

  1. Ze-Qiang Ma · Vanderbilt University Medical Center
  2. Matthew C. Chambers · Vanderbilt University Medical Center
  3. Amy-Joan L. Ham · Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center
  4. Kristin L. Cheek · Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center
  5. Corbin W. Whitwell · Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center
  6. Hans-Rudolf Aerni · Vanderbilt University, Vanderbilt University Medical Center
  7. Birgit Schilling · Buck Institute for Research on Aging
  8. Aaron W. Miller · Buck Institute for Research on Aging
  9. Richard M. Caprioli · Vanderbilt University, Vanderbilt University Medical Center
  10. David L. Tabb · Stellenbosch University, The Scripps Research Institute, University of Cape Town, Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt-Ingram Cancer Center

Methods and tools

  • ScanRanker: Ranks MS/MS spectra by sequence-tag quality to find high-quality unidentified spectra for de novo or cross-link analysis.

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