Change search
ReferencesLink to record
Permanent link

Direct link
Rapid and accurate peptide identification from tandem mass spectra
KTH, School of Biotechnology (BIO), Gene Technology.ORCID iD: 0000-0001-5689-9797
Show others and affiliations
2008 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 7, no 7, 3022-3027 p.Article in journal (Refereed) Published
Abstract [en]

Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification. Crux is implemented in C and is distributed with source code freely to noncommercial users.

Place, publisher, year, edition, pages
2008. Vol. 7, no 7, 3022-3027 p.
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:kth:diva-48852DOI: 10.1021/pr800127yISI: 000257449500041PubMedID: 18505281OAI: diva2:458747
QC 20111128Available from: 2011-11-23 Created: 2011-11-23 Last updated: 2012-02-23Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Käll, Lukas
By organisation
Gene Technology
In the same journal
Journal of Proteome Research
Bioinformatics (Computational Biology)

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 15 hits
ReferencesLink to record
Permanent link

Direct link