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

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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.

Author
George Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem
Date of publication
2016-01-05 14:31:42
Maintainer
George Rosenberger <rosenberger@imsb.biol.ethz.ch>
License
GPL (>= 3)
Version
1.3.3
URLs

View on CRAN

Man pages

AbsoluteQuantification
Absolute label-free quantification of mass spectrometry...
ALF
Generate ALF report
aLFQ.package
aLFQ
APEX
Training, testing and validation of APEX peptide...
apexFeatures
Calculation of physicochemical amino acid properties for APEX
APEXMS
Calculating absolute and relative protein abundance from mass...
import
import of mass spectrometry proteomics data analysis software...
LUDWIGMS
Estimation of Absolute Protein Quantities of Unlabeled...
PeptideInference
Peptide inference for aLFQ import data frame
ProteinInference
Protein inference for aLFQ import data frame
proteotypic
Prediction of the flyability of proteotypic peptides
UPS2MS
Calculating absolute and relative protein abundance from mass...

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