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aLFQ
View on CRAN: Click
here
Download and install aLFQ package within the R console
Install from CRAN:
install.packages("aLFQ")
Install from Github:
library("remotes")
install_github("cran/aLFQ") Install by package version:
library("remotes")
install_version("aLFQ", "1.3.6") Attach the package and use:
library("aLFQ")
Maintained by
George Rosenberger
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-09-13
Latest Update: 2020-01-08
Description:
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.
How to cite:
George Rosenberger (2013). aLFQ: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data. R package version 1.3.6, https://cran.r-project.org/web/packages/aLFQ. Accessed 05 Jun. 2026.
Previous versions and publish date:
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imports, suggests or enhances
Complete documentation for aLFQ
Functions, R codes and Examples using
the aLFQ R package
Some associated functions: ALF . APEX . APEXMS . AbsoluteQuantification . LUDWIGMS . PeptideInference . ProteinInference . UPS2MS . aLFQ.package . apexFeatures . import . proteotypic .
Some associated R codes: ALF.R . APEX.R . AbsoluteQuantification.R . ProteinInference.R . apexFeatures.R . import.R . proteotypic.R . Full aLFQ package functions and examples
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