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De novo peptide sequencing and identification with precision mass spectrometry
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences, MMS, Medical Mass Spectrometry.
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2007 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 6, no 1, 114-123 p.Article in journal (Refereed) Published
Abstract [en]

The recent proliferation of novel mass spectrometers such as Fourier transform, QTOF, and OrbiTrap marks a transition into the era of precision mass spectrometry, providing a 2 orders of magnitude boost to the mass resolution, as compared to low-precision ion-trap detectors. We investigate peptide de novo sequencing by precision mass spectrometry and explore some of the differences when compared to analysis of low-precision data. We demonstrate how the dramatically improved performance of de novo sequencing with precision mass spectrometry paves the way for novel approaches to peptide identification that are based on direct sequence lookups, rather than comparisons of spectra to a database. With the direct sequence lookup, it is not only possible to search a database very efficiently, but also to use the database in novel ways, such as searching for products of alternative splicing or products of fusion proteins in cancer. Our de novo sequencing software is available for download at http://peptide.ucsd.edu/.

Place, publisher, year, edition, pages
2007. Vol. 6, no 1, 114-123 p.
Keyword [en]
precision MS, MS/MS, de novo, database search, pattern matching, filtration, FTMS, FT-ICR, LTQ-FT
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-146543DOI: 10.1021/pr060271uISI: 000243262600011PubMedID: 17203955OAI: oai:DiVA.org:uu-146543DiVA: diva2:398412
Available from: 2011-02-17 Created: 2011-02-17 Last updated: 2017-12-11Bibliographically approved

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