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Improving automatic peptide mass fingerprint protein identification by combining many peak sets

Rognvaldsson, T; Häkkinen, Jari LU ; Lindberg, C; Marko-Varga, G; Potthast, Frank and Samuelsson, J (2004) In Journal of Chromatography. B 807(2). p.209-215
Abstract
An automated peak picking strategy is presented where several peak sets with different signal-to-noise levels are combined to form a more reliable statement on the protein identity. The strategy is compared against both manual peak picking and industry standard automated peak picking on a set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. The set of spectra contain samples ranging from strong to weak spectra, and the proposed multiple-scale method is shown to be much better on weak spectra than the industry standard method and a human operator, and equal in performance to these on strong and medium strong spectra. It is also demonstrated that peak sets selected by a human operator... (More)
An automated peak picking strategy is presented where several peak sets with different signal-to-noise levels are combined to form a more reliable statement on the protein identity. The strategy is compared against both manual peak picking and industry standard automated peak picking on a set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. The set of spectra contain samples ranging from strong to weak spectra, and the proposed multiple-scale method is shown to be much better on weak spectra than the industry standard method and a human operator, and equal in performance to these on strong and medium strong spectra. It is also demonstrated that peak sets selected by a human operator display a considerable variability and that it is impossible to speak of a single "true" peak set for a given spectrum. The described multiple-scale strategy both avoids time-consuming parameter tuning and exceeds the human operator in protein identification efficiency. The strategy therefore promises reliable automated user-independent protein identification using peptide mass fingerprints. (C) 2004 Elsevier B.V. All rights reserved. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
peak set combining, peptide mass fingerprinting, protein identification
in
Journal of Chromatography. B
volume
807
issue
2
pages
209 - 215
publisher
Elsevier
external identifiers
  • pmid:15203031
  • wos:000222283800006
  • scopus:2942529269
ISSN
1873-376X
DOI
10.1016/j.jchromb.2004.04.010
language
English
LU publication?
yes
id
2afcea6f-a0c3-4529-9263-89b44ce5757a (old id 273893)
date added to LUP
2007-10-31 08:42:25
date last changed
2017-01-01 05:17:47
@article{2afcea6f-a0c3-4529-9263-89b44ce5757a,
  abstract     = {An automated peak picking strategy is presented where several peak sets with different signal-to-noise levels are combined to form a more reliable statement on the protein identity. The strategy is compared against both manual peak picking and industry standard automated peak picking on a set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. The set of spectra contain samples ranging from strong to weak spectra, and the proposed multiple-scale method is shown to be much better on weak spectra than the industry standard method and a human operator, and equal in performance to these on strong and medium strong spectra. It is also demonstrated that peak sets selected by a human operator display a considerable variability and that it is impossible to speak of a single "true" peak set for a given spectrum. The described multiple-scale strategy both avoids time-consuming parameter tuning and exceeds the human operator in protein identification efficiency. The strategy therefore promises reliable automated user-independent protein identification using peptide mass fingerprints. (C) 2004 Elsevier B.V. All rights reserved.},
  author       = {Rognvaldsson, T and Häkkinen, Jari and Lindberg, C and Marko-Varga, G and Potthast, Frank and Samuelsson, J},
  issn         = {1873-376X},
  keyword      = {peak set combining,peptide mass fingerprinting,protein identification},
  language     = {eng},
  number       = {2},
  pages        = {209--215},
  publisher    = {Elsevier},
  series       = {Journal of Chromatography. B},
  title        = {Improving automatic peptide mass fingerprint protein identification by combining many peak sets},
  url          = {http://dx.doi.org/10.1016/j.jchromb.2004.04.010},
  volume       = {807},
  year         = {2004},
}