aLFQ: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data
Version 1.3.4

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.

Browse man pages Browse package API and functions Browse package files

AuthorGeorge Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem
Date of publication2017-03-23 15:28:19 UTC
MaintainerGeorge Rosenberger <rosenberger@imsb.biol.ethz.ch>
LicenseGPL (>= 3)
Version1.3.4
URL https://github.com/aLFQ
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("aLFQ")

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...

Functions

ALF Man page Source code
ALF.default Man page Source code
APEX Man page Source code
APEX.default Man page Source code
APEXMS Man page
APEX_LCQ Man page
APEX_ORBI Man page
AbsoluteQuantification Man page Source code
AbsoluteQuantification.default Man page Source code
LUDWIGMS Man page
LUDWIG_SRM Man page
PeptideInference Man page Source code
PeptideInference.default Man page Source code
ProteinInference Man page Source code
ProteinInference.default Man page Source code
UPS2 Man page
UPS2MS Man page
UPS2_LFQ Man page
UPS2_SC Man page
UPS2_SRM Man page
aLFQ Man page
aLFQ-package Man page
abacus_converter.import Source code
abacus_transform.import Source code
apexFeatures Man page Source code
apexFeatures.default Man page Source code
averageruns.import Source code
cval Man page Source code
cval.APEX Man page Source code
cval.AbsoluteQuantification Man page Source code
cval.default Man page Source code
export Man page Source code
export.AbsoluteQuantification Man page Source code
export.default Man page Source code
folderror.AbsoluteQuantification Source code
hist.AbsoluteQuantification Man page Source code
import Man page Source code
import.default Man page Source code
mprophet_converter.import Source code
openmslfq_converter.import Source code
openmslfq_transform.import Source code
openswath_converter.import Source code
pcfeatures.apexFeatures Source code
pepxml2csv_converter.import Source code
performanceplot.ALF Source code
pivot Man page Source code
pivot.AbsoluteQuantification Man page Source code
pivot.default Man page Source code
plot.APEX Man page Source code
plot.AbsoluteQuantification Man page Source code
predict.APEX Man page Source code
predict.AbsoluteQuantification Man page Source code
print.APEX Man page Source code
print.AbsoluteQuantification Man page Source code
print.apexFeatures Man page Source code
protein_inference.ProteinInference Source code
proteotypic Man page Source code
proteotypic.default Man page Source code
read_table.import Source code
scampi.ProteinInference Source code
skyline_converter.import Source code
strictnessfilter.ProteinInference Source code
stripsequence.import Source code
sumruns.import Source code
trypsin Source code
trypsin.default Source code
tune.ALF Source code

Files

COPYING
inst
inst/CITATION
inst/extdata
inst/extdata/example_concentration_protein.csv
inst/extdata/example_concentration_peptide.csv
inst/extdata/example.fasta
inst/extdata/example_openmslfq.csv
inst/extdata/example_abacus_protein.txt
inst/extdata/example_mprophet.txt
inst/extdata/UPS2.fasta
inst/extdata/example_skyline.csv
inst/extdata/example_openswath.txt
tests
tests/Examples
tests/Examples/aLFQ-Ex.Rout.save
tests/testthat.R
tests/testthat
tests/testthat/test_ProteinInference.R
tests/testthat/test_AbsoluteQuantification.R
tests/testthat/test_apexFeatures.R
NAMESPACE
data
data/APEXMS.rda
data/UPS2MS.rda
data/LUDWIGMS.rda
R
R/apexFeatures.R
R/proteotypic.R
R/import.R
R/ProteinInference.R
R/APEX.R
R/ALF.R
R/AbsoluteQuantification.R
MD5
DESCRIPTION
man
man/APEX.Rd
man/aLFQ.package.Rd
man/import.Rd
man/LUDWIGMS.Rd
man/APEXMS.Rd
man/proteotypic.Rd
man/AbsoluteQuantification.Rd
man/UPS2MS.Rd
man/ALF.Rd
man/PeptideInference.Rd
man/apexFeatures.Rd
man/ProteinInference.Rd
aLFQ documentation built on May 19, 2017, 10:37 p.m.