Package: aLFQ 1.3.6

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.

Authors:George Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem

aLFQ_1.3.6.tar.gz
aLFQ_1.3.6.zip(r-4.5)aLFQ_1.3.6.zip(r-4.4)aLFQ_1.3.6.zip(r-4.3)
aLFQ_1.3.6.tgz(r-4.4-any)aLFQ_1.3.6.tgz(r-4.3-any)
aLFQ_1.3.6.tar.gz(r-4.5-noble)aLFQ_1.3.6.tar.gz(r-4.4-noble)
aLFQ_1.3.6.tgz(r-4.4-emscripten)aLFQ_1.3.6.tgz(r-4.3-emscripten)
aLFQ.pdf |aLFQ.html✨
aLFQ/json (API)

# Install 'aLFQ' in R:
install.packages('aLFQ', repos = c('https://grosenberger.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • APEX_LCQ - Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
  • APEX_ORBI - Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
  • LUDWIG_SRM - Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry..
  • UPS2_LFQ - Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
  • UPS2_SC - Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
  • UPS2_SRM - Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

11 exports 1.45 score 88 dependencies 5 mentions 14 scripts 484 downloads

Last updated 5 years agofrom:b7957c9e2a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-winNOTESep 16 2024
R-4.5-linuxNOTESep 16 2024
R-4.4-winNOTESep 16 2024
R-4.4-macNOTESep 16 2024
R-4.3-winNOTESep 16 2024
R-4.3-macNOTESep 16 2024

Exports:AbsoluteQuantificationALFAPEXapexFeaturescvalexportimportPeptideInferencepivotProteinInferenceproteotypic

Dependencies:ade4bio3dbitopscaretcaToolsclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdplyre1071fansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergplotsgtablegtoolshardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellypillarpixmappkgconfigplyrpROCprodlimprogressrproxypurrrR6randomForestRColorBrewerRcppRcppArmadillorecipesreshape2rlangROCRrpartscalessegmentedseqinrshapespSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
aLFQaLFQ-package aLFQ
Absolute label-free quantification of mass spectrometry proteomics experimentsAbsoluteQuantification AbsoluteQuantification.default cval cval.AbsoluteQuantification cval.default export export.AbsoluteQuantification export.default hist.AbsoluteQuantification pivot pivot.AbsoluteQuantification pivot.default plot.AbsoluteQuantification predict.AbsoluteQuantification print.AbsoluteQuantification
Generate ALF reportALF ALF.default
Training, testing and validation of APEX peptide observability modelsAPEX APEX.default cval.APEX plot.APEX predict.APEX print.APEX
Calculation of physicochemical amino acid properties for APEXapexFeatures apexFeatures.default print.apexFeatures
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.APEXMS APEX_LCQ APEX_ORBI
import of mass spectrometry proteomics data analysis software reports.import import.default
Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry..LUDWIGMS LUDWIG_SRM
Peptide inference for aLFQ import data framePeptideInference PeptideInference.default
Protein inference for aLFQ import data frameProteinInference ProteinInference.default
Prediction of the flyability of proteotypic peptidesproteotypic proteotypic.default
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.UPS2 UPS2MS UPS2_LFQ UPS2_SC UPS2_SRM