On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications

Popis výsledku v původním jazyce

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

Název v anglickém jazyce

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications

Popis výsledku anglicky

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

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

<a href="/cs/project/GAP202%2F11%2F0968" target="_blank" >GAP202/11/0968: Podobnostní nemetrické vyhledávání v rozsáhlých komplexních databázích</a><br>

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2013

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Integrative Bioinformatics

ISSN

1613-4516

e-ISSN

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Svazek periodika

2013

Číslo periodika v rámci svazku

10/3

Stát vydavatele periodika

DE - Spolková republika Německo

Počet stran výsledku

15

Strana od-do

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Kód UT WoS článku

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EID výsledku v databázi Scopus

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