Advanced search
1 file | 1.21 MB

A complex standard for protein identification, designed by evolution

(2012) JOURNAL OF PROTEOME RESEARCH. 11(10). p.5065-5071
Author
Organization
Project
Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
HYPERTHERMOPHILE, PROTEOMICS, PEPTIDE IDENTIFICATION, MASS-SPECTROMETRY, PYROCOCCUS-FURIOSUS, OPEN SOURCE SOFTWARE, Pyrococcus furiosus, bioinformatics, peptide identification, protein identification, DATABASES, SEQUENCE, TANDEM, TOOLS

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 1.21 MB

Citation

Please use this url to cite or link to this publication:

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.
@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},
}

Altmetric
View in Altmetric
Web of Science
Times cited: