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A complex standard for protein identification, designed by evolution

Marc Vaudel, Julia M Burkhart, Daniela Breiter, René P Zahedi, Albert Sickmann and Lennart Martens UGent (2012) JOURNAL OF PROTEOME RESEARCH. 11(10). p.5065-5071
abstract
Shotgun proteomic investigations rely on the algorithmic assignment of mass spectra to peptides. The quality of these matches is therefore a cornerstone in the analysis and has been the subject of numerous recent developments. In order to establish the benefits of novel algorithms, they are applied to reference samples of known content. However, these were recently shown to be either too simple to resemble typical real-life samples or as leading to results of lower accuracy as the method itself. Here, we describe how to use the proteome of Pyrococcus furiosus, a hyperthermophile, as a standard to evaluate proteomics identification workflows. Indeed, we prove that the Pyrococcus furiosus proteome provides a valid method for detecting random hits, comparable to the decoy databases currently in popular use, but we also prove that the Pyrococcus furiosus proteome goes squarely beyond the decoy approach by also providing many hundreds of highly reliable true positive hits. Searching the Pyrococcus furiosus proteome can thus be used as a unique test that provides the ability to reliably detect both false positives as well as proteome-scale true positives, allowing the rigorous testing of identification algorithms at the peptide and protein level.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
HYPERTHERMOPHILE, PROTEOMICS, PEPTIDE IDENTIFICATION, MASS-SPECTROMETRY, PYROCOCCUS-FURIOSUS, OPEN SOURCE SOFTWARE, Pyrococcus furiosus, bioinformatics, peptide identification, protein identification, DATABASES, SEQUENCE, TANDEM, TOOLS
journal title
JOURNAL OF PROTEOME RESEARCH
J. Proteome Res.
volume
11
issue
10
pages
5065 - 5071
Web of Science type
Article
Web of Science id
000309441000028
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
5.056 (2012)
JCR rank
10/74 (2012)
JCR quartile
1 (2012)
ISSN
1535-3893
DOI
10.1021/pr300055q
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
3060573
handle
http://hdl.handle.net/1854/LU-3060573
date created
2012-11-26 15:27:14
date last changed
2016-12-19 15:43:05
@article{3060573,
  abstract     = {Shotgun proteomic investigations rely on the algorithmic assignment of mass spectra to peptides. The quality of these matches is therefore a cornerstone in the analysis and has been the subject of numerous recent developments. In order to establish the benefits of novel algorithms, they are applied to reference samples of known content. However, these were recently shown to be either too simple to resemble typical real-life samples or as leading to results of lower accuracy as the method itself. Here, we describe how to use the proteome of Pyrococcus furiosus, a hyperthermophile, as a standard to evaluate proteomics identification workflows. Indeed, we prove that the Pyrococcus furiosus proteome provides a valid method for detecting random hits, comparable to the decoy databases currently in popular use, but we also prove that the Pyrococcus furiosus proteome goes squarely beyond the decoy approach by also providing many hundreds of highly reliable true positive hits. Searching the Pyrococcus furiosus proteome can thus be used as a unique test that provides the ability to reliably detect both false positives as well as proteome-scale true positives, allowing the rigorous testing of identification algorithms at the peptide and protein level.},
  author       = {Vaudel, Marc and Burkhart, Julia M and Breiter, Daniela and Zahedi, Ren{\'e} P and Sickmann, Albert and Martens, Lennart},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {HYPERTHERMOPHILE,PROTEOMICS,PEPTIDE IDENTIFICATION,MASS-SPECTROMETRY,PYROCOCCUS-FURIOSUS,OPEN SOURCE SOFTWARE,Pyrococcus furiosus,bioinformatics,peptide identification,protein identification,DATABASES,SEQUENCE,TANDEM,TOOLS},
  language     = {eng},
  number       = {10},
  pages        = {5065--5071},
  title        = {A complex standard for protein identification, designed by evolution},
  url          = {http://dx.doi.org/10.1021/pr300055q},
  volume       = {11},
  year         = {2012},
}

Chicago
Vaudel, Marc, Julia M Burkhart, Daniela Breiter, René P Zahedi, Albert Sickmann, and Lennart Martens. 2012. “A Complex Standard for Protein Identification, Designed by Evolution.” Journal of Proteome Research 11 (10): 5065–5071.
APA
Vaudel, M., Burkhart, J. M., Breiter, D., Zahedi, R. P., Sickmann, A., & Martens, L. (2012). A complex standard for protein identification, designed by evolution. JOURNAL OF PROTEOME RESEARCH, 11(10), 5065–5071.
Vancouver
1.
Vaudel M, Burkhart JM, Breiter D, Zahedi RP, Sickmann A, Martens L. A complex standard for protein identification, designed by evolution. JOURNAL OF PROTEOME RESEARCH. 2012;11(10):5065–71.
MLA
Vaudel, Marc, Julia M Burkhart, Daniela Breiter, et al. “A Complex Standard for Protein Identification, Designed by Evolution.” JOURNAL OF PROTEOME RESEARCH 11.10 (2012): 5065–5071. Print.