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Originally published In Press as doi:10.1074/mcp.M700293-MCP200 on January 23, 2008.
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Molecular & Cellular Proteomics 7:962-970, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Comparison of Mascot and X!Tandem Performance for Low and High Accuracy Mass Spectrometry and the Development of an Adjusted Mascot Threshold*,S

Markus Brosch, Sajani Swamy, Tim Hubbard and Jyoti Choudhary{ddagger}

From The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom

It is a major challenge to develop effective sequence database search algorithms to translate molecular weight and fragment mass information obtained from tandem mass spectrometry into high quality peptide and protein assignments. We investigated the peptide identification performance of Mascot and X!Tandem for mass tolerance settings common for low and high accuracy mass spectrometry. We demonstrated that sensitivity and specificity of peptide identification can vary substantially for different mass tolerance settings, but this effect was more significant for Mascot. We present an adjusted Mascot threshold, which allows the user to freely select the best trade-off between sensitivity and specificity. The adjusted Mascot threshold was compared with the default Mascot and X!Tandem scoring thresholds and shown to be more sensitive at the same false discovery rates for both low and high accuracy mass spectrometry data.

{ddagger} To whom all correspondence should be addressed. E-mail: jc4{at}sanger.ac.uk






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