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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "aLFQ" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'aLFQ: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics
  Data'
version: 1.3.6
doi: 10.1093/bioinformatics/btu200
identifiers:
- type: doi
  value: 10.32614/CRAN.package.aLFQ
abstract: Determination of absolute protein quantities is necessary for multiple applications,
  such as mechanistic modeling of biological systems. Quantitative liquid chromatography
  tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance
  on a system-wide scale. To estimate absolute quantitative information using these
  relative abundance measurements requires additional information such as heavy-labeled
  references of known concentration. Multiple methods have been using different references
  and strategies; some are easily available whereas others require more effort on
  the users end. Hence, we believe the field might benefit from making some of these
  methods available under an automated framework, which also facilitates validation
  of the chosen strategy. We have implemented the most commonly used absolute label-free
  protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-,
  MS2-levels or spectral counts together with validation algorithms to enable automated
  data analysis and error estimation. Specifically, we used Monte-carlo cross-validation
  and bootstrapping for model selection and imputation of proteome-wide absolute protein
  quantity estimation. Our open-source software is written in the statistical programming
  language R and validated and demonstrated on a synthetic sample.
authors:
- family-names: Rosenberger
  given-names: George
  email: gr2578@cumc.columbia.edu
- family-names: Roest
  given-names: Hannes
- family-names: Ludwig
  given-names: Christina
- family-names: Aebersold
  given-names: Ruedi
- family-names: Malmstroem
  given-names: Lars
preferred-citation:
  type: article
  title: 'aLFQ: an R-package for estimating absolute protein quantities from label-free
    LC-MS/MS proteomics data'
  authors:
  - family-names: Rosenberger
    given-names: George
    email: gr2578@cumc.columbia.edu
  - family-names: Ludwig
    given-names: Christina
  - family-names: Roest
    given-names: Hannes L.
  - family-names: Aebersold
    given-names: Ruedi
  - family-names: Malmstroem
    given-names: Lars
  journal: Bioinformatics
  year: '2014'
  volume: '30'
  issue: '17'
  doi: 10.1093/bioinformatics/btu200
  url: https://academic.oup.com/bioinformatics/article/30/17/2511/2748144
  start: 2511-2513
repository: https://cran.r-universe.dev
repository-code: https://github.com/aLFQ
commit: b7957c9e2a77bf31031fa45d5d719a20ff0e43b4
url: https://github.com/aLFQ
date-released: '2020-01-07'
contact:
- family-names: Rosenberger
  given-names: George
  email: gr2578@cumc.columbia.edu