Identification of best indicators of peptide-spectrum match using a permutation resampling approach

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Fältnamn	Indikatorer	Metadata
000		03264naa a2200433 4500
001		oai:DiVA.org:uu-244598
003		SwePub
008		150218s2014 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2445982 URI
024	7	a https://doi.org/10.1142/S02197200144000102 DOI
040		a (SwePub)uu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Akhtar, Malik N.4 aut
245	1 0	a Identification of best indicators of peptide-spectrum match using a permutation resampling approach
264	1	c 2014
338		a electronic2 rdacarrier
500		a These authors contributed equally to this manuscript
520		a 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.
650	7	a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Farmaceutiska vetenskaper0 (SwePub)301012 hsv//swe
650	7	a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Pharmaceutical Sciences0 (SwePub)301012 hsv//eng
653		a Neuropeptides
653		a database search programs
653		a tandem MS
653		a p-value
653		a significance levels
653		a Ends permuted decoy database
653		a permutations
700	1	a Southey, Bruce R.4 aut
700	1	a Andrén, Per E.u Uppsala universitet,Institutionen för farmaceutisk biovetenskap4 aut0 (Swepub:uu)perandre
700	1	a Sweedler, Jonathan V.4 aut
700	1	a Rodriguez-Zas, Sandra L.4 aut
710	2	a Uppsala universitetb Institutionen för farmaceutisk biovetenskap4 org
773	0	t Journal of Bioinformatics and Computational Biologyg 12:5, s. 1440001-q 12:5<1440001-x 0219-7200x 1757-6334
856	4	u https://uu.diva-portal.org/smash/get/diva2:793390/FULLTEXT01.pdfx primaryx Raw objecty fulltext:print
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-244598
856	4 8	u https://doi.org/10.1142/S0219720014400010

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Av författaren/redakt...: Akhtar, Malik N.; Southey, Bruce R ...; Andrén, Per E.; Sweedler, Jonath ...; Rodriguez-Zas, S ...

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MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Medicinska och f ...; och Farmaceutiska ve ...

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Av lärosätet: Uppsala universitet

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