Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F12%3A10099576" target="_blank" >RIV/00216208:11320/12:10099576 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.jda.2011.10.003" target="_blank" >http://dx.doi.org/10.1016/j.jda.2011.10.003</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.jda.2011.10.003" target="_blank" >10.1016/j.jda.2011.10.003</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications

Popis výsledku v původním jazyce

In biological applications, the tandem mass spectrometry is a widely used method for determining protein and peptide sequences from an "in vitro" sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, whichis the output of the mass spectrometer. This work is focused on a similarity-search approach to mass spectra interpretation, where the parameterized Hausdorff distance (dHP) is used as the similarity. In order to provide an efficient similarity search under dHP, the metric access methods and the TriGen algorithm (controlling the metricity of dHP) are employed. Moreover, the search model based on the dHP supports posttranslational modifications (PTMs) in the query mass spectra, what is typically a problem when an indexing approach is used. Our approach can be utilized as a coarse filter by any other database approach for mass spectra interpretation.

Název v anglickém jazyce

Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications

Popis výsledku anglicky

In biological applications, the tandem mass spectrometry is a widely used method for determining protein and peptide sequences from an "in vitro" sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, whichis the output of the mass spectrometer. This work is focused on a similarity-search approach to mass spectra interpretation, where the parameterized Hausdorff distance (dHP) is used as the similarity. In order to provide an efficient similarity search under dHP, the metric access methods and the TriGen algorithm (controlling the metricity of dHP) are employed. Moreover, the search model based on the dHP supports posttranslational modifications (PTMs) in the query mass spectra, what is typically a problem when an indexing approach is used. Our approach can be utilized as a coarse filter by any other database approach for mass spectra interpretation.

Druh

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

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2012

Kód důvěrnosti údajů

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

Název periodika

Journal of Discrete Algorithms

ISSN

1570-8667

e-ISSN

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Svazek periodika

2012

Číslo periodika v rámci svazku

13

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

13

Strana od-do

19-31

Kód UT WoS článku

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EID výsledku v databázi Scopus

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