{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T11:10:40Z","timestamp":1776251440539,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Targeted data extraction methods are attractive ways to obtain quantitative peptide information from a proteomics experiment. Sequential Window Acquisition of all Theoretical Spectra (SWATH) and Data Independent Acquisition (DIA) methods increase reproducibility of acquired data because the classical precursor selection is omitted and all present precursors are fragmented. However, especially for targeted data extraction, MS coordinates (retention time information precursor and fragment masses) are required for the particular entities (peptide ions). These coordinates are usually generated in a so-called discovery experiment earlier on in the project if not available in public spectral library repositories. The quality of the assay panel is crucial to ensure appropriate downstream analysis. For that, a method is needed to create spectral libraries and to export customizable assay panels.<\/jats:p>\n               <jats:p>Results: Here, we present a versatile set of functions to generate assay panels from spectral libraries for use in targeted data extraction methods (SWATH\/DIA) in the area of proteomics.<\/jats:p>\n               <jats:p>Availability and implementation: specL is implemented in the R language and available under an open-source license (GPL-3) in Bioconductor since BioC 3.0 (R-3.1) http:\/\/www.bioconductor.org (Trachsel et\u00a0al., 2015). A vignette with a complete tutorial describing data import\/export and analysis is included in the package and can also be found as supplement material of this article.<\/jats:p>\n               <jats:p>Contact: \u00a0cp@fgcz.ethz.ch or jg@fgcz.ethz.ch<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv105","type":"journal-article","created":{"date-parts":[[2015,2,26]],"date-time":"2015-02-26T08:54:32Z","timestamp":1424940872000},"page":"2228-2231","source":"Crossref","is-referenced-by-count":12,"title":["specL\u2014an R\/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics"],"prefix":"10.1093","volume":"31","author":[{"given":"Christian","family":"Panse","sequence":"first","affiliation":[{"name":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Trachsel","sequence":"additional","affiliation":[{"name":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonas","family":"Grossmann","sequence":"additional","affiliation":[{"name":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralph","family":"Schlapbach","sequence":"additional","affiliation":[{"name":"Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,2,23]]},"reference":[{"key":"2023020202133372300_btv105-B1","author":"Bernhardt","year":"2012"},{"key":"2023020202133372300_btv105-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nmeth.2329","article-title":"Method of the year 2012","volume":"10","author":"Editorial","year":"2013","journal-title":"Nat. Methods"},{"key":"2023020202133372300_btv105-B3","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1002\/pmic.201100463","article-title":"Using iRT, a normalized retention time for more targeted measurement of peptides","volume":"12","author":"Escher","year":"2012","journal-title":"Proteomics"},{"key":"2023020202133372300_btv105-B4","first-page":"13.7","article-title":"Using BiblioSpec for creating and searching tandem MS peptide libraries","volume":"13","author":"Frewen","year":"2007","journal-title":"Curr. Protoc. Bioinform."},{"key":"2023020202133372300_btv105-B5","doi-asserted-by":"crossref","first-page":"O111","DOI":"10.1074\/mcp.O111.016717","article-title":"Targeted data extraction of the MS\/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis","volume":"11","author":"Gillet","year":"2012","journal-title":"Mol. Cell Proteomics"},{"key":"2023020202133372300_btv105-B6","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1038\/nmeth.2702","article-title":"Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition","volume":"10","author":"Lambert","year":"2013","journal-title":"Nat. Methods"},{"key":"2023020202133372300_btv105-B7","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating and analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020202133372300_btv105-B8","volume-title":"BiocParallel: Bioconductor Facilities for Parallel Evaluation","author":"Morgan","year":"2015"},{"key":"2023020202133372300_btv105-B9","volume-title":"protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics","author":"Panse","year":"2015"},{"key":"2023020202133372300_btv105-B10","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/nature11835","article-title":"A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis","volume":"494","author":"Picotti","year":"2013","journal-title":"Nature"},{"key":"2023020202133372300_btv105-B11","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/nbt.2841","article-title":"OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data","volume":"32","author":"Rost","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2023020202133372300_btv105-B12","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.chom.2013.04.008","article-title":"The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis","volume":"13","author":"Schubert","year":"2013","journal-title":"Cell Host Microbe"},{"key":"2023020202133372300_btv105-B13","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/nprot.2015.015","article-title":"Building high-quality assay libraries for targeted analysis of SWATH MS data","volume":"10","author":"Schubert","year":"2015","journal-title":"Nat. Protoc."},{"key":"2023020202133372300_btv105-B14","volume-title":"specL: Prepare Peptide Spectrum Matches for Use in Targeted Proteomics","author":"Trachsel","year":"2015"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/13\/2228\/49034437\/bioinformatics_31_13_2228.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/13\/2228\/49034437\/bioinformatics_31_13_2228.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:39:46Z","timestamp":1675309186000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/13\/2228\/195976"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,2,23]]},"references-count":14,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2015,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv105","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,7,1]]},"published":{"date-parts":[[2015,2,23]]}}}