title: specL--an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  METHODS
  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 al., 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.
  
  
  BACKGROUND
  cp@fgcz.ethz.ch or jg@fgcz.ethz.ch
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Panse
authors.affiliation: Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: Trachsel
authors.affiliation: Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland.
authors.forename: Jonas
authors.initials: J
authors.lastname: Grossmann
authors.affiliation: Functional Genomics Center Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland.
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
mesh_terms: D006801:Humans; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry*; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010446:Peptide Fragments; D011506:Proteins