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, 25 (17), 2174-80

Automated Protein (Re)sequencing With MS/MS and a Homologous Database Yields Almost Full Coverage and Accuracy

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Automated Protein (Re)sequencing With MS/MS and a Homologous Database Yields Almost Full Coverage and Accuracy

Xiaowen Liu et al. Bioinformatics.

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.

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