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  • 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. aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Here, we provide aLFQ, an open-source implementation of algorithms supporting the estimation of protein quantities by any of the aforementioned methods, and additionally provide automated workflows for data analysis and error estimation. aLFQ was implemented in R as a modular S3 package.
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