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 publication2017-03-23 15:28:19 UTC
MaintainerGeorge Rosenberger <rosenberger@imsb.biol.ethz.ch>
LicenseGPL (>= 3)
Version1.3.4
https://github.com/aLFQ

View on CRAN

Functions

AbsoluteQuantification Man page
AbsoluteQuantification.default Man page
ALF Man page
ALF.default Man page
aLFQ Man page
aLFQ-package Man page
APEX Man page
APEX.default Man page
apexFeatures Man page
apexFeatures.default Man page
APEX_LCQ Man page
APEXMS Man page
APEX_ORBI Man page
cval Man page
cval.AbsoluteQuantification Man page
cval.APEX Man page
cval.default Man page
export Man page
export.AbsoluteQuantification Man page
export.default Man page
hist.AbsoluteQuantification Man page
import Man page
import.default Man page
LUDWIGMS Man page
LUDWIG_SRM Man page
PeptideInference Man page
PeptideInference.default Man page
pivot Man page
pivot.AbsoluteQuantification Man page
pivot.default Man page
plot.AbsoluteQuantification Man page
plot.APEX Man page
predict.AbsoluteQuantification Man page
predict.APEX Man page
print.AbsoluteQuantification Man page
print.APEX Man page
print.apexFeatures Man page
ProteinInference Man page
ProteinInference.default Man page
proteotypic Man page
proteotypic.default Man page
UPS2 Man page
UPS2_LFQ Man page
UPS2MS Man page
UPS2_SC Man page
UPS2_SRM Man page

Files

aLFQ
aLFQ/COPYING
aLFQ/inst
aLFQ/inst/CITATION
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/testthat.R
aLFQ/tests/testthat
aLFQ/tests/testthat/test_ProteinInference.R
aLFQ/tests/testthat/test_AbsoluteQuantification.R
aLFQ/tests/testthat/test_apexFeatures.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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.