title: aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.
abstract: BACKGROUND
  The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user-friendly and transparent software supporting large-scale absolute protein quantification has been lacking.
  
  
  RESULTS
  We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation.
  
  
  METHODS
  aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321).
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: George
authors.initials: G
authors.lastname: Rosenberger
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Christina
authors.initials: C
authors.lastname: Ludwig
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Hannes L
authors.initials: HL
authors.lastname: Röst
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D011506:Proteins
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