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specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics


Panse, Christian; Trachsel, Christian; Grossmann, Jonas; Schlapbach, Ralph (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics, 31(13):2228-2231.

Abstract

MOTIVATION Targeted data extraction methods are attractive ways to obtain quantitative peptide information from a proteomics experiment. SWATH (Sequential Window Acquisition of all Theoretical Spectra) and DIA (Data Independent Acquisition) 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 customisable assay panels. 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. Availability: 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, Panse, and Grossmann, 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 paper. CONTACT cp@fgcz.ethz.ch,jg@fgcz.ethz.ch.

Abstract

MOTIVATION Targeted data extraction methods are attractive ways to obtain quantitative peptide information from a proteomics experiment. SWATH (Sequential Window Acquisition of all Theoretical Spectra) and DIA (Data Independent Acquisition) 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 customisable assay panels. 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. Availability: 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, Panse, and Grossmann, 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 paper. CONTACT cp@fgcz.ethz.ch,jg@fgcz.ethz.ch.

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3 citations in Web of Science®
3 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Language:English
Date:23 February 2015
Deposited On:05 Mar 2015 14:20
Last Modified:08 Dec 2017 12:25
Publisher:Oxford University Press
ISSN:1367-4803
Publisher DOI:https://doi.org/10.1093/bioinformatics/btv105
PubMed ID:25712692

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