Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments
DC Field | Value | Language |
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dc.contributor.author | Li, Honglan | - |
dc.contributor.author | Park, Jonghun | - |
dc.contributor.author | Kim, Hyunwoo | - |
dc.contributor.author | Hwang, Kyu-Baek | - |
dc.contributor.author | Paek, Eunok | - |
dc.date.available | 2018-05-08T14:40:15Z | - |
dc.date.created | 2018-04-17 | - |
dc.date.issued | 2017-06 | - |
dc.identifier.issn | 1535-3893 | - |
dc.identifier.uri | http://scholarworks.bwise.kr/ssu/handle/2018.sw.ssu/6347 | - |
dc.description.abstract | Proteogenoinit searches are useful for novel peptide identification from tandem mass spectra. Usually, separate and multistage approaches are adopted to accurately control the false discovery rate (FDR) for: proteogenomic search. Their performance on novel peptide identification has not been thoroughly evaluated; however, mainly due to the. difficulty in Confirming existence of identified novel peptides.' We, simulated a proteogenomic search controlled, spike-in proteomic data set. After confirming that the results of the simulated proteogenomic search were similar to those of a real proteogenomic search using,a human cell line data set, we evaluated the performance of six FDR Control methods-global, separate, and multistage FDR estimation) respectively, coupled to a target-decoy search and a mixture model-based: method on novel peptide identification. The multistage approach showed the highest accuracy for FDR. estimation. However, global and separate FDR estimation with the mixture model-based method showed higher sensitivities than others at the same true FDR. Furthermore, the mixture model based method performed equally well when applied without or with a reduced set of decoy sequences: Considering different prior probabilities for novel and known protein identification, we recommend using mixture model-based methods with separate FDR estimation for sensitive and reliable identification of novel peptides from proteogenomic searches. | - |
dc.publisher | AMER CHEMICAL SOC | - |
dc.relation.isPartOf | JOURNAL OF PROTEOME RESEARCH | - |
dc.subject | DATABASE SEARCH | - |
dc.subject | MASS-SPECTROMETRY | - |
dc.subject | SEQUENCE DATABASE | - |
dc.subject | PEPTIDES | - |
dc.subject | CANCER | - |
dc.subject | IDENTIFICATIONS | - |
dc.subject | MS/MS | - |
dc.subject | TOOL | - |
dc.title | Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments | - |
dc.type | Article | - |
dc.identifier.doi | 10.1021/acs.jproteome.7b00033 | - |
dc.type.rims | ART | - |
dc.identifier.bibliographicCitation | JOURNAL OF PROTEOME RESEARCH, v.16, no.6, pp.2231 - 2239 | - |
dc.description.journalClass | 1 | - |
dc.identifier.wosid | 000402850800011 | - |
dc.identifier.scopusid | 2-s2.0-85020171156 | - |
dc.citation.endPage | 2239 | - |
dc.citation.number | 6 | - |
dc.citation.startPage | 2231 | - |
dc.citation.title | JOURNAL OF PROTEOME RESEARCH | - |
dc.citation.volume | 16 | - |
dc.contributor.affiliatedAuthor | Hwang, Kyu-Baek | - |
dc.type.docType | Article | - |
dc.description.isOpenAccess | N | - |
dc.subject.keywordAuthor | proteogenomic search | - |
dc.subject.keywordAuthor | novel peptide identification | - |
dc.subject.keywordAuthor | spike-in data | - |
dc.subject.keywordAuthor | simulation | - |
dc.subject.keywordAuthor | false discovery rate control | - |
dc.subject.keywordPlus | DATABASE SEARCH | - |
dc.subject.keywordPlus | MASS-SPECTROMETRY | - |
dc.subject.keywordPlus | SEQUENCE DATABASE | - |
dc.subject.keywordPlus | PEPTIDES | - |
dc.subject.keywordPlus | CANCER | - |
dc.subject.keywordPlus | IDENTIFICATIONS | - |
dc.subject.keywordPlus | MS/MS | - |
dc.subject.keywordPlus | TOOL | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
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