Tyck till om SwePub Sök
här!
Sökning: onr:"swepub:oai:DiVA.org:uu-240011" >
Accurate Assignment...
-
Akhtar, Malik N.
(författare)
Accurate Assignment of Significance to Neuropeptide Identifications Using Monte Carlo K-Permuted Decoy Databases
- Artikel/kapitelEngelska2014
Förlag, utgivningsår, omfång ...
-
2014-10-17
-
Public Library of Science (PLoS),2014
-
electronicrdacarrier
Nummerbeteckningar
-
LIBRIS-ID:oai:DiVA.org:uu-240011
-
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-240011URI
-
https://doi.org/10.1371/journal.pone.0111112DOI
Kompletterande språkuppgifter
-
Språk:engelska
-
Sammanfattning på:engelska
Ingår i deldatabas
Klassifikation
-
Ämneskategori:ref swepub-contenttype
-
Ämneskategori:art swepub-publicationtype
Anmärkningar
-
In support of accurate neuropeptide identification in mass spectrometry experiments, novel Monte Carlo permutation testing was used to compute significance values. Testing was based on k-permuted decoy databases, where k denotes the number of permutations. These databases were integrated with a range of peptide identification indicators from three popular open-source database search software (OMSSA, Crux, and X! Tandem) to assess the statistical significance of neuropeptide spectra matches. Significance p-values were computed as the fraction of the sequences in the database with match indicator value better than or equal to the true target spectra. When applied to a test-bed of all known manually annotated mouse neuropeptides, permutation tests with k-permuted decoy databases identified up to 100% of the neuropeptides at p-value < 10(-5). The permutation test p-values using hyperscore (X! Tandem), E-value (OMSSA) and Sp score (Crux) match indicators outperformed all other match indicators. The robust performance to detect peptides of the intuitive indicator "number of matched ions between the experimental and theoretical spectra" highlights the importance of considering this indicator when the p-value was borderline significant. Our findings suggest permutation decoy databases of size 1x10(5) are adequate to accurately detect neuropeptides and this can be exploited to increase the speed of the search. The straightforward Monte Carlo permutation testing (comparable to a zero order Markov model) can be easily combined with existing peptide identification software to enable accurate and effective neuropeptide detection. The source code is available at http://stagbeetle.animal.uiuc.edu/pepshop/MSMSpermutationtesting.
Ämnesord och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
-
Southey, Bruce R.
(författare)
-
Andrén, Per E.Uppsala universitet,Institutionen för farmaceutisk biovetenskap(Swepub:uu)perandre
(författare)
-
Sweedler, Jonathan V.
(författare)
-
Rodriguez-Zas, Sandra L.
(författare)
-
Uppsala universitetInstitutionen för farmaceutisk biovetenskap
(creator_code:org_t)
Sammanhörande titlar
-
Ingår i:PLOS ONE: Public Library of Science (PLoS)9:10, s. e111112-1932-6203
Internetlänk
Hitta via bibliotek
-
PLOS ONE
(Sök värdpublikationen i LIBRIS)
Till lärosätets databas