||42 (Research article)
||Rosenberger, George; Ludwig, Christina; Röst, Hannes; Aebersold, Ruedi; Malmström, Lars
||aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.
||Bioinformatics (2014) 30(17) 2511-3
||66 citations (journal impact: 4.62)
||MOTIVATIONThe 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.RESULTSWe 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.AVAILABILITYaLFQ is written in R and freely available under the GPLv3 from CRAN httpwww.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.
||We describe a software package for R that estimates absolute protein quantities from mass spectrometry data.