On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F13%3A10139361" target="_blank" >RIV/00216208:11320/13:10139361 - isvavai.cz</a>
Result on the web
<a href="http://journal.imbio.de/article.php?aid=228" target="_blank" >http://journal.imbio.de/article.php?aid=228</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.2390/biecoll-jib-2013-228" target="_blank" >10.2390/biecoll-jib-2013-228</a>
Alternative languages
Result language
angličtina
Original language name
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications
Original language description
The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisyquery spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter isused as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient datab
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
IN - Informatics
OECD FORD branch
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Result continuities
Project
<a href="/en/project/GAP202%2F11%2F0968" target="_blank" >GAP202/11/0968: Large-scale Nonmetric Similarity Search in Complex Domains</a><br>
Continuities
S - Specificky vyzkum na vysokych skolach
Others
Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Integrative Bioinformatics
ISSN
1613-4516
e-ISSN
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Volume of the periodical
2013
Issue of the periodical within the volume
10/3
Country of publishing house
DE - GERMANY
Number of pages
15
Pages from-to
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UT code for WoS article
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EID of the result in the Scopus database
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