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Identification of best indicators of peptide-spectrum match using a permutation resampling approach
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
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2014 (English)In: Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, Vol. 12, no 5, 1440001- p.Article in journal (Refereed) Published
Abstract [en]

Various indicators of observed-theoretical spectrum matches were compared and the resulting statistical significance was characterized using permutation resampling. Novel decoy databases built by resampling the terminal positions of peptide sequences were evaluated to identify the conditions for accurate computation of peptide match significance levels. The methodology was tested on real and manually curated tandem mass spectra from peptides across a wide range of sizes. Spectra match indicators from complementary database search programs were pro filed and optimal indicators were identified. The combination of the optimal indicator and permuted decoy databases improved the calculation of the peptide match significance compared to the approaches currently implemented in the database search programs that rely on distributional assumptions. Permutation tests using p-values obtained from software-dependent matching scores and E-values outperformed permutation tests using all other indicators. The higher overlap in matches between the database search programs when using end permutation compared to existing approaches con firmed the superiority of the end permutation method to identify peptides. The combination of effective match indicators and the end permutation method is recommended for accurate detection of peptides.

Place, publisher, year, edition, pages
2014. Vol. 12, no 5, 1440001- p.
Keyword [en]
Neuropeptides, database search programs, tandem MS, p-value, significance levels, Ends permuted decoy database, permutations
National Category
Pharmaceutical Sciences
URN: urn:nbn:se:uu:diva-244598DOI: 10.1142/S0219720014400010ISI: 000348347600002PubMedID: 25362838OAI: oai:DiVA.org:uu-244598DiVA: diva2:793390

These authors contributed equally to this manuscript

Available from: 2015-03-06 Created: 2015-02-18 Last updated: 2015-03-06Bibliographically approved

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Andrén, Per E.
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