2009/06/17 by Xiaowen Liu, Yonghua Han, Denis Yuen +1 · 4 citations
Chemistry · Biochemistry, Genetics and Molecular Biology · #Advanced Proteomics Techniques and Applications #Mass Spectrometry Techniques and Applications #Genomics and Phylogenetic Studies
paper · pdf · doi:10.1093/bioinformatics/btp366
openalex publication_date 2009/06/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22
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. Availability: The software, named Champs (Complete Homology-Assisted Ms/ms Protein Sequencing), and the MS/MS data used in the article, are freely available at http://monod.uwaterloo.ca/champs/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.