Improving the Similarity Search of Tandem Mass Spectra using Metric Access Methods

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F10%3A10033415" target="_blank" >RIV/00216208:11320/10:10033415 - isvavai.cz</a>

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Improving the Similarity Search of Tandem Mass Spectra using Metric Access Methods

Popis výsledku v původním jazyce

The tandem mass spectrometry is a widely used method for determining protein sequences from an "in vitro" sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, which is the output of the mass spectrometer.This work is focused on a similarity-search approach to mass spectra interpretation, where the parametrized 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 are employed. We show that similarity search using dHP exhibits better correctness of interpretation than the cosine similarity commonly mentioned in mass spectrometry literature. Moreover, the search model using the dHP distance could be extended to support chemical modifications in the query mass spectra, which is typically a problem when the cosine similarity is used. Our approach can be utilized as a coarse filter by any other database approach for mass spectra in

Název v anglickém jazyce

Improving the Similarity Search of Tandem Mass Spectra using Metric Access Methods

Popis výsledku anglicky

The tandem mass spectrometry is a widely used method for determining protein sequences from an "in vitro" sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, which is the output of the mass spectrometer.This work is focused on a similarity-search approach to mass spectra interpretation, where the parametrized 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 are employed. We show that similarity search using dHP exhibits better correctness of interpretation than the cosine similarity commonly mentioned in mass spectrometry literature. Moreover, the search model using the dHP distance could be extended to support chemical modifications in the query mass spectra, which is typically a problem when the cosine similarity is used. Our approach can be utilized as a coarse filter by any other database approach for mass spectra in

Druh

D - Stať ve sborníku

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

<a href="/cs/project/GA201%2F09%2F0683" target="_blank" >GA201/09/0683: Vyhledávání v rozsáhlých multimediálních databázích</a><br>

Návaznosti

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

Rok uplatnění

2010

Kód důvěrnosti údajů

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

Název statě ve sborníku

Third International Conference on Similarity Search and Applications

ISBN

978-1-4503-0420-7

ISSN

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e-ISSN

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Počet stran výsledku

8

Strana od-do

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Název nakladatele

ACM

Místo vydání

Istanbul, Turkey

Místo konání akce

Istanbul, Turkey

Datum konání akce

18. 9. 2010

Typ akce podle státní příslušnosti

EUR - Evropská akce

Kód UT WoS článku

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