Data Self-Recalibration and Mixture Mass Fingerprint Searching (DASER-MMF) to enhance protein identification within complex mixtures.

Journal of the American Society for Mass Spectrometry
Ryan M DanellChristoph H Borchers

Abstract

A novel algorithm based on Data Self-Recalibration and a subsequent Mixture Mass Fingerprint search (DASER-MMF) has been developed to improve the performance of protein identification from online 1D and 2D-LC-MS/MS experiments conducted on high-resolution mass spectrometers. Recalibration of 40% to 75% of the MS spectra in a human serum dataset is demonstrated with average errors of 0.3 +/- 0.3 ppm, regardless of the original calibration quality. With simple protein mixtures, the MMF search identifies new proteins not found in the MS/MS based search and increases the sequence coverage for identified proteins by six times. The high mass accuracy allows proteins to be identified with as little as three peptide mass hits. When applied to very complex samples, the MMF search shows less dramatic performance improvements. However, refinements such as additional discriminating factors utilized within the search space provide significant gains in protein identification ability and indicate that further enhancements are possible in this realm.

References

Dec 1, 1984·Analytical Chemistry·E B LedfordM L Gross
Oct 13, 1998·Mass Spectrometry Reviews·A G MarshallG S Jackson
Jan 5, 2001·Analytical Chemistry·P B O'Connor, C E Costello
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Sang-Won LeeRichard D Smith
Mar 20, 2003·Journal of Proteome Research·James X PangGregory J Opitek
Sep 5, 2003·Journal of the American Society for Mass Spectrometry·William J HenzelJohn T Stults
Dec 25, 2003·Journal of Proteome Research·Ji GaoStanley A Hefta
Jun 1, 1993·Current Biology : CB·D J PappinA J Bleasby
Nov 3, 2004·BioTechniques·Ljiljana Pasa-TolićRichard D Smith
Mar 29, 2005·Journal of the American Society for Mass Spectrometry·Nathan K KaiserJames E Bruce
Jun 28, 2005·Journal of the American Society for Mass Spectrometry·Angela D NorbeckRichard D Smith
Aug 29, 2006·Journal of the American Society for Mass Spectrometry·Richard L Wong, I Jonathan Amster
Sep 22, 2006·Rapid Communications in Mass Spectrometry : RCM·Magnus PalmbladRainer Cramer

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