Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy

peer-reviewed · Bioinformatics · 2009

peer-reviewed · Bioinformatics · 2009. Xiaowen Liu et al. Motivation The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for…
Date 2009-09-01
Type peer-reviewed
Venue Bioinformatics
Publisher Oxford University Press (OUP)
Contribution adjacent
DOI 10.1093/bioinformatics/btp366
Citations (OpenAlex) 39
Venue 2-year citedness 6.16

Abstract

Motivation The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem. Results Very often, although the target protein is novel, it has a homologous protein included in a known database. When this happens, we propose a novel algorithm and automated software tool, named Champs, for sequencing the complete protein from MS/MS data of a few enzymatic digestions of the purified protein. Validation with two standard proteins showed that our automated method yields >99% sequence coverage and 100% sequence accuracy on these two proteins. Our method is useful to sequence novel proteins or ‘re-sequence’ a protein that has mutations comparing with the database protein sequence.

Authors

  1. Xiaowen Liu · Indiana University Indianapolis, Indiana University School of Medicine, Indiana University-Purdue University Indianapolis, Tulane University, University of Waterloo
  2. Yonghua Han · University of Western Ontario, Western University
  3. Denis Yuen · Bioinformatics Solutions Inc., University of Waterloo
  4. Bin Ma · Rapid Novor Inc., University of Waterloo, University of Western Ontario, Western University

Methods and tools

  • Champs: Sequences a complete novel protein by de novo sequencing its peptides and then assembling them against a HOMOLOGOUS database rather than an exact one, reaching near-full coverage and accuracy where neither approach alone would.

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Cited by (26)

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