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Author Good, David M. ♦ Wenger, Craig D. ♦ McAlister, Graeme C. ♦ Bai, Dina L. ♦ Hunt, Donald F. ♦ Coon, Joshua J.
Source SpringerLink
Content type Text
Publisher Springer-Verlag
File Format PDF
Copyright Year ©2009
Language English
Subject Domain (in DDC) Natural sciences & mathematics ♦ Chemistry & allied sciences
Subject Keyword Analytical Chemistry ♦ Biotechnology ♦ Organic Chemistry ♦ Proteomics ♦ Bioinformatics
Abstract Tandem mass spectra (MS/MS) produced using electron transfer dissociation (ETD) differ from those derived from collision-activated dissociation (CAD) in several important ways. Foremost, the predominant fragment ion series are different: c- and z $^{·}$-type ions are favored in ETD spectra while b- and y-type ions comprise the bulk of the fragments in CAD spectra. Additionally, ETD spectra possess charge-reduced precursors and unique neutral losses. Most database search algorithms were designed to analyze CAD spectra, and have only recently been adapted to accommodate c- and z $^{·}$-type ions; therefore, inclusion of these additional spectral features can hinder identification, leading to lower confidence scores and decreased sensitivity. Because of this, it is important to pre-process spectral data before submission to a database search to remove those features that cause complications. Here, we demonstrate the effects of removing these features on the number of unique peptide identifications at a 1% false discovery rate (FDR) using the open mass spectrometry search algorithm (OMSSA). When analyzing two biologic replicates of a yeast protein extract in three total analyses, the number of unique identifications with a ∼1% FDR increased from 4611 to 5931 upon spectral pre-processing—an increase of ∼28. 6%. We outline the most effective pre-processing methods, and provide free software containing these algorithms.
ISSN 10440305
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2009-03-14
Publisher Institution The American Society for Mass Spectrometry
Publisher Place New York
e-ISSN 18791123
Journal Journal of The American Society for Mass Spectrometry
Volume Number 20
Issue Number 8
Page Count 6
Starting Page 1435
Ending Page 1440


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Source: SpringerLink