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dc.contributor.authorHas, Canan
dc.contributor.authorKundakçı, Cemal Ulaş
dc.contributor.authorAltay, Aybuge
dc.contributor.authorAllmer, Jens
dc.date.accessioned2017-04-17T09:04:13Z
dc.date.available2017-04-17T09:04:13Z
dc.date.issued2013
dc.identifier.citationHas, C., Kundakçı, C. U., Altay, A., and Allmer, J. (2013, September 25-27). Ranking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matches. Paper presented at the 8th International Symposium on Health Informatics and Bioinformatics. doi:10.1109/HIBIT.2013.6661686en_US
dc.identifier.isbn9781479907014
dc.identifier.urihttp://doi.org/10.1109/HIBIT.2013.6661686
dc.identifier.urihttp://hdl.handle.net/11147/5321
dc.description8th International Symposium on Health Informatics and Bioinformatics, HIBIT 2013; Ankara; Turkey; 25 September 2013 through 27 September 2013en_US
dc.description.abstractProteomics is currently driven by mass spectrometry. For the analysis of tandem mass spectra many computational algorithms have been proposed. There are two approaches, one which assigns a peptide sequence to a tandem mass spectrum directly and one which employs a sequence database for looking up possible solutions. The former method needs high quality spectra while the latter can tolerate lower quality spectra. Since both methods are computationally expensive, it is sensible to establish spectral quality using an independent fast algorithm. In this study, we first establish proper settings for database search algorithms for the analysis of spectra in our gold benchmark dataset and then analyze the performance of ScanRanker, an algorithm for quality assessment of tandem MS spectra, on this ground truth data. We found that OMSSA and MSGFDB have limitations in their scoring functions but were able to form a proper consensus prediction using majority vote for our benchmark data. Unfortunately, ScanRanker's results do not correlate well with the consensus and ScanRanker is also too slow to be used in the capacity it is supposed to be used. © 2013 IEEEen_US
dc.language.isoengen_US
dc.publisherIEEEen_US
dc.relation.isversionof10.1109/HIBIT.2013.6661686en_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectDatabase sizeen_US
dc.subjectFalse discovery rateen_US
dc.subjectMass spectrometryen_US
dc.subjectScanRankeren_US
dc.subjectScoring algorithmen_US
dc.subjectSpectrum qualifyen_US
dc.titleRanking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matchesen_US
dc.typeconferenceObjecten_US
dc.contributor.authorIDTR114186en_US
dc.contributor.authorIDTR107974en_US
dc.contributor.iztechauthorHas, Canan
dc.contributor.iztechauthorKundakçı, Cemal Ulaş
dc.contributor.iztechauthorAltay, Aybuge
dc.contributor.iztechauthorAllmer, Jens
dc.relation.journal8th International Symposium on Health Informatics and Bioinformaticsen_US
dc.contributor.departmentİYTE, Fen Fakültesi, Moleküler Biyoloji ve Genetik Bölümüen_US
dc.identifier.scopusSCOPUS:2-s2.0-84892634324
dc.relation.publicationcategoryKonferans Öğesi - Uluslararası - Kurum Öğretim Elemanıen_US


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