# Processing of adductomic mass spectral datasets

## Documentation for package ‘adductomicsR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

adductQuant | Adduct quantification for adductomicsR
AdductQuantif-class | AdductQuantif class The AdductQuantif class contains a peak integral matrix, peak ranges and region of integration, the isotopic distribution identified for each integrated peak and the target table of peaks integrated.
AdductSpec-class | AdductSpec class
adductSpecGen | Constructor of AdductSpec object deconvolute spectra MS2 and MS1 levels
c-method | AdductQuantif class The AdductQuantif class contains a peak integral matrix, peak ranges and region of integration, the isotopic distribution identified for each integrated peak and the target table of peaks integrated.
c-method | AdductSpec class
digestMod | modified 'Digest' function (from OrgMassSpecR package)
dotProdMatrix | dot product matrix calculation
dotProdSpectra | dot product calculation
dynamicNoiseFilter | Dynamic Noise filtration
filterAdductTable | filter samples with low QC and features with large missing values Removes adducts that have not been integrated with many missing values and provides QC on samples
findPeaks | identify peaks
generateTargTable | Make a target table for adductomicsR quantificaton using specSimPep results
groupMS2spec,rtDevModels,sumAdductType,Parameters,AdductSpec-class | AdductSpec class
groupMS2spec-method | AdductSpec class
IsotopicDistributionMod | modified function from package OrgMassSpecR
loessWrapperMod | wrapper script for loess modeling
ms2Group | group MS/MS precursor masses
nAdjPeaks | remove lower intensity adjacent peaks
outputPeakTable | output peak table from AdductQuantif object
peakIdData,predIsoDist,targTable,AdductQuantif,AdductQuantif-class | AdductQuantif class The AdductQuantif class contains a peak integral matrix, peak ranges and region of integration, the isotopic distribution identified for each integrated peak and the target table of peaks integrated.
peakIdQuant_newMethod | Adduct Peak quant
peakIntegrate | integrate a peak from a peak table with peak start and peak end retention times
peakListId | peak list Identification
peakRangeSum | raw eic signal intensity and mass summation and spike removal.
Peptides,specPepMatches,AdductSpec-class | AdductSpec class
predIsoDist-method | AdductQuantif class The AdductQuantif class contains a peak integral matrix, peak ranges and region of integration, the isotopic distribution identified for each integrated peak and the target table of peaks integrated.
probPeaks | potentially problematic peak identification
retentionCorr | loess-based retention time deviation correction
rtDevModelling | MS/MS spectrum grouping and retention time deviation modelling for adductomicsR
rtDevModelSave | extract and save retention time deviation models from adductSpec class object
show,c,file.paths,peakQuantTable,AdductQuantif,AdductQuantif-class | AdductQuantif class The AdductQuantif class contains a peak integral matrix, peak ranges and region of integration, the isotopic distribution identified for each integrated peak and the target table of peaks integrated.
show,c,Specfile.paths,adductMS2spec,metaData,AdductSpec-class | AdductSpec class
signalGrouping | Signal grouping
specPepMatches-method | AdductSpec class
specSimPepId | spectral similarity based adducted peptide identification for adductomicsR
spectraCreate | Deconvolute both MS2 and MS1 levels scans adductomics
truePeakTrough | true peak and trough detection
x | AdductSpec class