aLFQ: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data

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.

AuthorGeorge Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem
Date of publication2016-01-05 14:31:42
MaintainerGeorge Rosenberger <rosenberger@imsb.biol.ethz.ch>
LicenseGPL (>= 3)
Version1.3.3
https://github.com/aLFQ

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Files in this package

aLFQ
aLFQ/COPYING
aLFQ/inst
aLFQ/inst/CITATION
aLFQ/inst/tests
aLFQ/inst/tests/test_ProteinInference.R
aLFQ/inst/tests/test_AbsoluteQuantification.R
aLFQ/inst/tests/test_apexFeatures.R
aLFQ/inst/extdata
aLFQ/inst/extdata/example_concentration_protein.csv
aLFQ/inst/extdata/example_concentration_peptide.csv
aLFQ/inst/extdata/example.fasta
aLFQ/inst/extdata/example_openmslfq.csv
aLFQ/inst/extdata/example_abacus_protein.txt
aLFQ/inst/extdata/example_mprophet.txt
aLFQ/inst/extdata/UPS2.fasta
aLFQ/inst/extdata/example_skyline.csv
aLFQ/inst/extdata/example_openswath.txt
aLFQ/tests
aLFQ/tests/Examples
aLFQ/tests/Examples/aLFQ-Ex.Rout.save
aLFQ/tests/units.R
aLFQ/NAMESPACE
aLFQ/data
aLFQ/data/APEXMS.rda
aLFQ/data/UPS2MS.rda
aLFQ/data/LUDWIGMS.rda
aLFQ/R
aLFQ/R/apexFeatures.R aLFQ/R/proteotypic.R aLFQ/R/import.R aLFQ/R/ProteinInference.R aLFQ/R/APEX.R aLFQ/R/ALF.R aLFQ/R/AbsoluteQuantification.R
aLFQ/MD5
aLFQ/DESCRIPTION
aLFQ/man
aLFQ/man/APEX.Rd aLFQ/man/aLFQ.package.Rd aLFQ/man/import.Rd aLFQ/man/LUDWIGMS.Rd aLFQ/man/APEXMS.Rd aLFQ/man/proteotypic.Rd aLFQ/man/AbsoluteQuantification.Rd aLFQ/man/UPS2MS.Rd aLFQ/man/ALF.Rd aLFQ/man/PeptideInference.Rd aLFQ/man/apexFeatures.Rd aLFQ/man/ProteinInference.Rd

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