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Title: Ranking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matches
Authors: Has, Canan
Kundakçı, Cemal Ulaş
Altay, Aybuge
Allmer, Jens
Keywords: Database size
False discovery rate
Mass spectrometry
Scoring algorithm
Spectrum qualify
Publisher: Institute of Electrical and Electronics Engineers Inc.
Source: Has, 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.2013.6661686
Abstract: Proteomics 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 IEEE
Description: 8th International Symposium on Health Informatics and Bioinformatics, HIBIT 2013; Ankara; Turkey; 25 September 2013 through 27 September 2013
ISBN: 9781479907014
Appears in Collections:Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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