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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/273893
- author
- Rognvaldsson, T
; Häkkinen, Jari
LU
; Lindberg, C
; Marko-Varga, G
; Potthast, Frank
and Samuelsson, J
- organization
- publishing date
- 2004
- 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
- pmid:15203031
- 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
- 2016-04-01 12:36:35
- date last changed
- 2025-04-04 14:49:14
@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}},
keywords = {{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}},
doi = {{10.1016/j.jchromb.2004.04.010}},
volume = {{807}},
year = {{2004}},
}