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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 ScanRanker 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 | URI: | http://doi.org/10.1109/HIBIT.2013.6661686 http://hdl.handle.net/11147/5321 |
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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