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| Fältnamn | Indikatorer | Metadata |
|---|---|---|
| 000 | 03425naa a2200361 4500 | |
| 001 | oai:DiVA.org:uu-240011 | |
| 003 | SwePub | |
| 008 | 150105s2014 | |||||||||||000 ||eng| | |
| 024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2400112 URI |
| 024 | 7 | a https://doi.org/10.1371/journal.pone.01111122 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 Accurate Assignment of Significance to Neuropeptide Identifications Using Monte Carlo K-Permuted Decoy Databases |
| 264 | c 2014-10-17 | |
| 264 | 1 | b Public Library of Science (PLoS),c 2014 |
| 338 | a electronic2 rdacarrier | |
| 520 | a 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. | |
| 650 | 7 | a NATURVETENSKAPx Kemi0 (SwePub)1042 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Chemical Sciences0 (SwePub)1042 hsv//eng |
| 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 PLOS ONEd : Public Library of Science (PLoS)g 9:10, s. e111112-q 9:10<e111112-x 1932-6203 |
| 856 | 4 | u https://uu.diva-portal.org/smash/get/diva2:775892/FULLTEXT01.pdfx primaryx Raw objecty fulltext:print |
| 856 | 4 | u https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0111112&type=printable |
| 856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-240011 |
| 856 | 4 8 | u https://doi.org/10.1371/journal.pone.0111112 |
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