proFIA: Preprocessing of FIA-HRMS data

Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and generate the peak table. The workflow includes noise modelling, band detection and filtering then signal matching and missing value imputation. The peak table can then be exported as a .tsv file for further analysis. Visualisations to assess the quality of the data and of the signal made are easely produced.

Author
Alexis Delabriere and Etienne Thevenot.
Date of publication
None
Maintainer
Alexis Delabriere <alexis.delabriere@cea.fr>
License
CeCILL
Version
1.0.10

View on Bioconductor

Man pages

acquisitionDirectory
Create a table containg the classes of the acquisition.
analyzeAcquisitionFIA
Wrapper function for the full FIA analysis workflow.
determiningSizePeak.Geom
Determine the limits of the injection peak in a FIA...
estimateNoiseListFiles
Estimate the noise of multiple MS acquisition.
exportDataMatrix-proFIAset-method
Export data matrix.
exportExpressionSet-proFIAset-method
Export proFIAset to ExpressionSet
exportPeakTable-proFIAset-method
Export proFIAset as a peak table.
exportSampleMetadata-proFIAset-method
Export samples metadata.
exportVariableMetadata-proFIAset-method
Export variable metadata.
fillPeaks.WKNN-proFIAset-method
Fill missing values in the peak table.
findBandsFIA
Detect band in a FIA acquisition
findFIAsignal
Detect peaks in an FIA acquisition.
findMzGroup-proFIAset-method
find a group in a FIA experiment.
getInjectionPeak
Fit an injection peak to an FIA acquisition.
group.FIA-proFIAset-method
Group the peaks of an FIA acquisition.
makeDataMatrix-proFIAset-method
Construct the data matrix of a proFIAset object.
noiseEstimation-class
An S4 class to represent heteroscedasctic noise of MS.
peaksGroup-proFIAset-method
Return the peaks corresponding to a group.
plotEICs-proFIAset-method
Plot raw temporal profiles of the selected group.
plotInjectionPeaks-proFIAset-method
Plot the injection peaks of a proFIAset object.
plotNoise
Plot the estimated noise from a proFIAset object.
plotRaw-proFIAset-method
plotting of raw data
proFIA-package
Process FIA-HRMS datasets.
proFIAset
Process FIA experiment.
proFIAset-class
An S4 class to represent an FIA experiments.

Files in this package

proFIA/.BBSoptions
proFIA/DESCRIPTION
proFIA/NAMESPACE
proFIA/NEWS
proFIA/R
proFIA/R/Denoising.R
proFIA/R/cWrapper.R
proFIA/R/classContainer.R
proFIA/R/fastMatchPpm.R
proFIA/R/findPeaksFIA.R
proFIA/R/methodsContainer.R
proFIA/R/noiseEstimator.R
proFIA/R/proFIA-package.R
proFIA/build
proFIA/build/vignette.rds
proFIA/inst
proFIA/inst/CITATION
proFIA/inst/NEWS
proFIA/inst/doc
proFIA/inst/doc/proFIA-vignette.R
proFIA/inst/doc/proFIA-vignette.Rmd
proFIA/inst/doc/proFIA-vignette.html
proFIA/inst/unitTests
proFIA/inst/unitTests/test_proFIA.R
proFIA/man
proFIA/man/acquisitionDirectory.Rd
proFIA/man/analyzeAcquisitionFIA.Rd
proFIA/man/determiningSizePeak.Geom.Rd
proFIA/man/estimateNoiseListFiles.Rd
proFIA/man/exportDataMatrix-proFIAset-method.Rd
proFIA/man/exportExpressionSet-proFIAset-method.Rd
proFIA/man/exportPeakTable-proFIAset-method.Rd
proFIA/man/exportSampleMetadata-proFIAset-method.Rd
proFIA/man/exportVariableMetadata-proFIAset-method.Rd
proFIA/man/fillPeaks.WKNN-proFIAset-method.Rd
proFIA/man/findBandsFIA.Rd
proFIA/man/findFIAsignal.Rd
proFIA/man/findMzGroup-proFIAset-method.Rd
proFIA/man/getInjectionPeak.Rd
proFIA/man/group.FIA-proFIAset-method.Rd
proFIA/man/makeDataMatrix-proFIAset-method.Rd
proFIA/man/noiseEstimation-class.Rd
proFIA/man/peaksGroup-proFIAset-method.Rd
proFIA/man/plotEICs-proFIAset-method.Rd
proFIA/man/plotInjectionPeaks-proFIAset-method.Rd
proFIA/man/plotNoise.Rd
proFIA/man/plotRaw-proFIAset-method.Rd
proFIA/man/proFIA-package.Rd
proFIA/man/proFIAset-class.Rd
proFIA/man/proFIAset.Rd
proFIA/src
proFIA/src/FIABandsExtractionCentroid.c
proFIA/src/UtilFunc.c
proFIA/src/UtilFunc.h
proFIA/src/fastMatchPpm.c
proFIA/tests
proFIA/tests/runTests.R
proFIA/vignettes
proFIA/vignettes/proFIA-vignette.Rmd
proFIA/vignettes/proFIA-vignette.bib
proFIA/vignettes/workflow_info.png