$,MChromatograms-method	MChromatograms-class
$,pSet-method	pSet-class
$<-,MChromatograms-method	MChromatograms-class
$<-,pSet-method	pSet-class
abstract,MIAPE-method	MIAPE-class
abstract,pSet-method	pSet-class
acquisitionNum	Spectrum-class
acquisitionNum,MSnSet-method	MSnSet-class
acquisitionNum,MSpectra-method	MSpectra
acquisitionNum,OnDiskMSnExp-method	OnDiskMSnExp-class
acquisitionNum,pSet-method	pSet-class
acquisitionNum,Spectrum-method	Spectrum-class
addFeaturesOfInterest	FeaturesOfInterest-class
addFeaturesOfInterest,FeaturesOfInterest,FoICollection-method	FeaturesOfInterest-class
addFeaturesOfInterest-methods	FeaturesOfInterest-class
addIdentificationData	addIdentificationData-methods
addIdentificationData,MSnExp,character-method	MSnExp-class
addIdentificationData,MSnExp,data.frame-method	MSnExp-class
addIdentificationData,MSnExp,mzID-method	MSnExp-class
addIdentificationData,MSnExp,mzIDClasses-method	MSnExp-class
addIdentificationData,MSnExp,mzIDCollection-method	MSnExp-class
addIdentificationData,MSnExp,mzRident-method	MSnExp-class
addIdentificationData,MSnSet,character-method	MSnSet-class
addIdentificationData,MSnSet,data.frame-method	MSnSet-class
addIdentificationData,MSnSet,mzID-method	MSnSet-class
addIdentificationData,MSnSet,mzIDClasses-method	MSnSet-class
addIdentificationData,MSnSet,mzIDCollection-method	MSnSet-class
addIdentificationData,MSnSet,mzRident-method	MSnSet-class
addIdentificationData-methods	addIdentificationData-methods
addMSnSetMetadata	MSnSet-class
aggregationFun	Chromatogram-class
aggvar	aggvar
alignRt,Chromatogram,Chromatogram-method	Chromatogram-class
alignRt,MChromatograms,Chromatogram-method	MChromatograms-class
all.equal,MSnExp,MSnExp-method	MSnExp-class
all.equal,MSnExp,OnDiskMSnExp-method	MSnExp-class
all.equal,OnDiskMSnExp,MSnExp-method	MSnExp-class
all.equal,OnDiskMSnExp,OnDiskMSnExp-method	MSnExp-class
analyser	MIAPE-class
analyser,MIAPE-method	MIAPE-class
analyser,MSnSet-method	MSnSet-class
analyser,pSet-method	pSet-class
analyserDetails	MIAPE-class
analyserDetails,MIAPE-method	MIAPE-class
analyserDetails,pSet-method	pSet-class
analyzer	MIAPE-class
analyzer,MIAPE-method	MIAPE-class
analyzer,MSnSet-method	MSnSet-class
analyzer,pSet-method	pSet-class
analyzerDetails	MIAPE-class
analyzerDetails,MIAPE-method	MIAPE-class
analyzerDetails,pSet-method	pSet-class
as	mzRident2dfr
as.data.frame,Chromatogram-method	Chromatogram-class
as.data.frame.MSnExp	MSnExp-class
as.data.frame.MSnSet	MSnSet-class
as.data.frame.mzRident	mzRident2dfr
as.data.frame.Spectrum	Spectrum-class
as.ExpressionSet.MSnSet	MSnSet-class
as.matrix.FoICollection	FeaturesOfInterest-class
as.MIAME.MIAPE	MIAPE-class
as.MSnExp.OnDiskMSnExp	OnDiskMSnExp-class
as.MSnSet.ExpressionSet	MSnSet-class
assayData,OnDiskMSnExp-method	OnDiskMSnExp-class
assayData,pSet-method	pSet-class
averageMSnSet	averageMSnSet
bin	bin-methods
bin,Chromatogram-method	Chromatogram-class
bin,MChromatograms-method	MChromatograms-class
bin,MSnExp-method	MSnExp-class
bin,OnDiskMSnExp-method	OnDiskMSnExp-class
bin,Spectrum-method	Spectrum-class
bin-methods	bin-methods
bpi	OnDiskMSnExp-class
bpi,OnDiskMSnExp-method	OnDiskMSnExp-class
c,MChromatograms-method	MChromatograms-class
calculateFragments	calculateFragments-methods
calculateFragments,character,missing-method	calculateFragments-methods
calculateFragments,character,Spectrum2-method	Spectrum2-class
centroided	Spectrum-class
centroided,MSpectra-method	MSpectra
centroided,OnDiskMSnExp-method	OnDiskMSnExp-class
centroided,pSet-method	pSet-class
centroided,Spectrum-method	Spectrum-class
centroided<-	Spectrum-class
centroided<-,OnDiskMSnExp,logical-method	OnDiskMSnExp-class
centroided<-,pSet,ANY-method	pSet-class
centroided<-,pSet,logical-method	pSet-class
centroided<-,Spectrum,ANY-method	Spectrum-class
centroided<-,Spectrum,logical-method	Spectrum-class
Chromatogram	Chromatogram-class
chromatogram	chromatogram-MSnExp-method
chromatogram,MSnExp-method	chromatogram-MSnExp-method
Chromatogram-class	Chromatogram-class
class:MIAPE	MIAPE-class
class:MSnExp	MSnExp-class
class:MSnProcess	MSnProcess-class
class:MSnSet	MSnSet-class
class:MzTab	MzTab-class
class:NAnnotatedDataFrame	defunct
class:OnDiskMSnExp	OnDiskMSnExp-class
class:pSet	pSet-class
class:ReporterIons	ReporterIons-class
class:Spectrum	Spectrum-class
class:Spectrum1	Spectrum1-class
class:Spectrum2	Spectrum2-class
clean	clean-methods
clean,Chromatogram-method	Chromatogram-class
clean,MChromatograms-method	MChromatograms-class
clean,MSnExp-method	MSnExp-class
clean,MSpectra-method	MSpectra
clean,OnDiskMSnExp-method	OnDiskMSnExp-class
clean,Spectrum-method	Spectrum-class
clean-methods	clean-methods
coerce,AnnotatedDataFrame,list-method	pSet-class
coerce,ExpressionSet,MSnSet-method	MSnSet-class
coerce,FoICollection,matrix-method	FeaturesOfInterest-class
coerce,IBSpectra,MSnSet-method	MSnSet-class
coerce,matrix,MChromatograms-method	MChromatograms-class
coerce,MIAPE,MIAME-method	MIAPE-class
coerce,MIAxE,list-method	pSet-class
coerce,MSmap,data.frame-method	MSmap-class
coerce,MSnExp,data.frame-method	MSnExp-class
coerce,MSnExp,MSpectra-method	MSnExp-class
coerce,MSnProcess,list-method	MSnProcess-class
coerce,MSnSet,data.frame-method	MSnSet-class
coerce,MSnSet,ExpressionSet-method	MSnSet-class
coerce,MSnSet,SummarizedExperiment-method	MSnSet-class
coerce,MSpectra,list-method	MSpectra
coerce,MSpectra,MSnExp-method	MSpectra
coerce,mzRident,data.frame-method	readMzIdData
coerce,MzTab,MSnSetList-method	MzTab-class
coerce,OnDiskMSnExp,MSnExp-method	OnDiskMSnExp-class
coerce,Spectrum,data.frame-method	Spectrum-class
coerce,SummarizedExperiment,MSnSet-method	MSnSet-class
collisionEnergy	Spectrum2-class
collisionEnergy,MSpectra-method	MSpectra
collisionEnergy,OnDiskMSnExp-method	OnDiskMSnExp-class
collisionEnergy,pSet-method	pSet-class
collisionEnergy,Spectrum-method	Spectrum2-class
colnames<-,MChromatograms-method	MChromatograms-class
combine,MIAPE,MIAPE-method	MIAPE-class
combine,MSnProcess,MSnProcess-method	MSnProcess-class
combine,MSnSet,MSnSet-method	MSnSet-class
combineFeatures	combineFeatures
combineFeatures,MSnSet-method	combineFeatures
combineSpectra	combineSpectra
combineSpectra,MSnExp-method	combineSpectra
combineSpectra,MSpectra-method	combineSpectra
combineSpectraMovingWindow	combineSpectraMovingWindow
comments	MzTab-class
common	FeatComp-class
common,FeatComp-method	FeatComp-class
common,methods	FeatComp-class
commonFeatureNames	commonFeatureNames
compareChromatograms	Chromatogram-class
compareChromatograms,Chromatogram,Chromatogram-method	Chromatogram-class
compareChromatograms,MChromatograms,MChromatograms-method	MChromatograms-class
compareChromatograms,MChromatograms,missing-method	MChromatograms-class
compareMSnSets	compareMSnSets
compareSpectra	compareSpectra-methods
compareSpectra,MSnExp,missing-method	MSnExp-class
compareSpectra,OnDiskMSnExp,missing-method	OnDiskMSnExp-class
compareSpectra,Spectrum,Spectrum-method	Spectrum-class
compareSpectra-methods	compareSpectra-methods
compfnames	FeatComp-class
compfnames,list,missing-method	FeatComp-class
compfnames,MSnSet,MSnSet-method	FeatComp-class
compfnames-methods	FeatComp-class
consensusSpectrum	consensusSpectrum
defaultNeutralLoss	calculateFragments-methods
description,FeaturesOfInterest-method	FeaturesOfInterest-class
description,FoICollection-method	FeaturesOfInterest-class
description,MSnSet-method	MSnSet-class
description,pSet-method	pSet-class
description,ReporterIons-method	ReporterIons-class
detectorType	MIAPE-class
detectorType,MIAPE-method	MIAPE-class
detectorType,MSnSet-method	MSnSet-class
detectorType,pSet-method	pSet-class
dim	pSet-class
dim,MSmap-method	MSmap-class
dim,MSnSet-method	MSnSet-class
dim,NAnnotatedDataFrame-method	defunct
dim,pSet-method	pSet-class
droplevels.MSnSet	MSnSet-class
estimateMzResolution	estimateMzResolution
estimateMzResolution,MSnExp-method	estimateMzResolution
estimateMzResolution,Spectrum-method	estimateMzResolution
estimateMzScattering	estimateMzScattering
estimateNoise	estimateNoise-method
estimateNoise,MSnExp-method	MSnExp-class
estimateNoise,OnDiskMSnExp-method	OnDiskMSnExp-class
estimateNoise,Spectrum-method	Spectrum-class
estimateNoise-methods	estimateNoise-method
executeProcessingStep	ProcessingStep-class
expandFeatureVars	fData-utils
expemail	MIAPE-class
expemail,MIAPE-method	MIAPE-class
expemail,MSnSet-method	MSnSet-class
expemail,pSet-method	pSet-class
experimentData,pSet-method	pSet-class
experimentData<-,MSnSet,MIAPE-method	MSnSet-class
expinfo,MIAPE-method	MIAPE-class
exprs,MSnSet-method	MSnSet-class
exptitle	MIAPE-class
exptitle,MIAPE-method	MIAPE-class
exptitle,MSnSet-method	MSnSet-class
exptitle,pSet-method	pSet-class
extractPrecSpectra	extractPrecSpectra-methods
extractPrecSpectra,MSnExp,numeric-method	MSnExp-class
extractPrecSpectra,MSnExp-method	MSnExp-class
extractPrecSpectra,OnDiskMSnExp,numeric-method	OnDiskMSnExp-class
extractPrecSpectra-methods	extractPrecSpectra-methods
extractSpectra	defunct
extractSpectraData	extractSpectraData
factorsAsStrings	factorsAsStrings
fData,MChromatograms-method	MChromatograms-class
fData,MSnSetList-method	MSnSetList-class
fData,pSet-method	pSet-class
fData<-,MChromatograms,ANY-method	MChromatograms-class
fData<-,MSnSet,data.frame-method	MSnSet-class
fData<-,MSnSetList,DataFrame-method	MSnSetList-class
fData<-,pSet,data.frame-method	pSet-class
FeatComp-class	FeatComp-class
featureCV	featureCV
featureData,MChromatograms-method	MChromatograms-class
featureData,pSet-method	pSet-class
featureData<-,MChromatograms,ANY-method	MChromatograms-class
featureNames,MChromatograms-method	MChromatograms-class
featureNames,OnDiskMSnExp-method	OnDiskMSnExp-class
featureNames,pSet-method	pSet-class
featureNames<-,MChromatograms-method	MChromatograms-class
featureNames<-,OnDiskMSnExp,ANY-method	OnDiskMSnExp-class
featureNames<-,OnDiskMSnExp-method	OnDiskMSnExp-class
FeaturesOfInterest	FeaturesOfInterest-class
FeaturesOfInterest,character,character,missing-method	FeaturesOfInterest-class
FeaturesOfInterest,character,character,MSnSet-method	FeaturesOfInterest-class
FeaturesOfInterest-class	FeaturesOfInterest-class
FeaturesOfInterest-methods	FeaturesOfInterest-class
fileName,MSmap-method	MSmap-class
fileName,MzTab-method	MzTab-class
fileNames	pSet-class
fileNames,MSmap-method	MSmap-class
fileNames,MSnProcess-method	MSnProcess-class
fileNames,MSnSet-method	MSnSet-class
fileNames,MzTab-method	MzTab-class
fileNames,pSet-method	pSet-class
fillUp	fillUp
filterAcquisitionNum	MSnExp-class
filterAcquisitionNum,MSnExp-method	MSnExp-class
filterAcquisitionNum,OnDiskMSnExp-method	MSnExp-class
filterEmptySpectra	MSnExp-class
filterEmptySpectra,MSnExp-method	MSnExp-class
filterEmptySpectra,OnDiskMSnExp-method	MSnExp-class
filterFile	MSnExp-class
filterFile,MSnExp-method	MSnExp-class
filterFile,OnDiskMSnExp-method	MSnExp-class
filterIdentificationDataFrame	filterIdentificationDataFrame
filterIntensity,Chromatogram-method	Chromatogram-class
filterIntensity,MChromatograms-method	MChromatograms-class
filterIsolationWindow	MSnExp-class
filterIsolationWindow,MSnExp-method	MSnExp-class
filterMsLevel	MSnExp-class
filterMsLevel,MSnExp-method	MSnExp-class
filterMsLevel,MSnSet-method	MSnSet-class
filterMsLevel,MSpectra-method	MSpectra
filterMsLevel,OnDiskMSnExp-method	MSnExp-class
filterMz	trimMz-methods
filterMz,MSnExp-method	MSnExp-class
filterMz,MSpectra-method	MSpectra
filterMz,OnDiskMSnExp-method	MSnExp-class
filtermz,Spectrum,numeric-method	Spectrum-class
filterMz,Spectrum-method	Spectrum-class
filterMz-methods	trimMz-methods
filterNA	MSnSet-class
filterNA,matrix-method	MSnSet-class
filterNA,MSnSet-method	MSnSet-class
filterPolarity	MSnExp-class
filterPolarity,MSnExp-method	MSnExp-class
filterPolarity,OnDiskMSnExp-method	MSnExp-class
filterPrecursorMz	MSnExp-class
filterPrecursorMz,MSnExp-method	MSnExp-class
filterPrecursorScan	MSnExp-class
filterPrecursorScan,MSnExp-method	MSnExp-class
filterPrecursorScan,OnDiskMSnExp-method	MSnExp-class
filterRt	MSnExp-class
filterRt,Chromatogram-method	Chromatogram-class
filterRt,MSnExp-method	MSnExp-class
filterRt,OnDiskMSnExp-method	MSnExp-class
filterZero	MSnSet-class
filterZero,matrix-method	MSnSet-class
filterZero,MSnSet-method	MSnSet-class
fnamesIn	FeaturesOfInterest-class
fnamesIn,FeaturesOfInterest,data.frame-method	FeaturesOfInterest-class
fnamesIn,FeaturesOfInterest,matrix-method	FeaturesOfInterest-class
fnamesIn,FeaturesOfInterest,MSnSet-method	FeaturesOfInterest-class
fnamesIn-methods	FeaturesOfInterest-class
foi	FeaturesOfInterest-class
foi,FeaturesOfInterest-method	FeaturesOfInterest-class
foi,FoICollection-method	FeaturesOfInterest-class
foi-methods	FeaturesOfInterest-class
FoICollection	FeaturesOfInterest-class
FoICollection,list-method	FeaturesOfInterest-class
FoICollection,missing-method	FeaturesOfInterest-class
FoICollection-class	FeaturesOfInterest-class
FoICollection-methods	FeaturesOfInterest-class
formatRt	formatRt
fromFile	Spectrum-class
fromFile,Chromatogram-method	Chromatogram-class
fromFile,MSnSet-method	MSnSet-class
fromFile,MSpectra-method	MSpectra
fromFile,OnDiskMSnExp-method	OnDiskMSnExp-class
fromFile,pSet-method	pSet-class
fromFile,Spectrum-method	Spectrum-class
fvarLabels,MChromatograms-method	MChromatograms-class
fvarLabels,pSet-method	pSet-class
fvarMetadata,pSet-method	pSet-class
get.amino.acids	get.amino.acids
get.atomic.mass	get.atomic.mass
getEcols	grepEcols
getVariableName	getVariableName
grepEcols	grepEcols
hasChromatograms	hasSpectraOrChromatograms
hasSpectra	hasSpectraOrChromatograms
header	pSet-class
header,OnDiskMSnExp,missing-method	OnDiskMSnExp-class
header,OnDiskMSnExp,numeric-method	OnDiskMSnExp-class
header,pSet,missing-method	pSet-class
header,pSet,numeric-method	pSet-class
idSummary	MSnSet-class
idSummary,MSnExp-method	MSnExp-class
idSummary,MSnSet-method	MSnSet-class
image,MSnSet-method	MSnSet-class
image2	MSnSet-class
imageNA2	imageNA2
impute,MSnSet-method	impute
instrumentCustomisations	MIAPE-class
instrumentCustomisations,MIAPE-method	MIAPE-class
instrumentCustomisations,pSet-method	pSet-class
instrumentManufacturer	MIAPE-class
instrumentManufacturer,MIAPE-method	MIAPE-class
instrumentManufacturer,pSet-method	pSet-class
instrumentModel	MIAPE-class
instrumentModel,MIAPE-method	MIAPE-class
instrumentModel,pSet-method	pSet-class
intensity	Spectrum-class
intensity,Chromatogram-method	Chromatogram-class
intensity,MSpectra-method	MSpectra
intensity,OnDiskMSnExp-method	OnDiskMSnExp-class
intensity,pSet-method	pSet-class
intensity,Spectrum-method	Spectrum-class
ionCount	Spectrum-class
ionCount,MSpectra-method	MSpectra
ionCount,OnDiskMSnExp-method	OnDiskMSnExp-class
ionCount,pSet-method	pSet-class
ionCount,Spectrum-method	Spectrum-class
ionSource	MIAPE-class
ionSource,MIAPE-method	MIAPE-class
ionSource,MSnSet-method	MSnSet-class
ionSource,pSet-method	pSet-class
ionSourceDetails	MIAPE-class
ionSourceDetails,MIAPE-method	MIAPE-class
ionSourceDetails,pSet-method	pSet-class
iPQF	iPQF
is.na.MSnSet	plotNA-methods
isCentroided	Spectrum-class
isCentroided,MSnExp-method	MSnExp-class
isCentroided,MSpectra-method	MSpectra
isCentroided,OnDiskMSnExp-method	OnDiskMSnExp-class
isCentroided,Spectrum-method	Spectrum-class
isCentroidedFromFile	isCentroidedFromFile
isEmpty,Chromatogram-method	Chromatogram-class
isEmpty,environment-method	Spectrum-class
isEmpty,MChromatograms-method	MChromatograms-class
isEmpty,MSpectra-method	MSpectra
isEmpty,Spectrum-method	Spectrum-class
isMSnbaseFastLoad	MSnbaseOptions
isMSnbaseVerbose	MSnbaseOptions
isolationWindow,MSnExp-method	MSnExp-class
isolationWindowLowerMz	pSet-class
isolationWindowLowerMz,OnDiskMSnExp-method	OnDiskMSnExp-class
isolationWindowLowerMz,pSet-method	pSet-class
isolationWindowUpperMz	pSet-class
isolationWindowUpperMz,OnDiskMSnExp-method	OnDiskMSnExp-class
isolationWindowUpperMz,pSet-method	pSet-class
iTRAQ4	iTRAQ4
iTRAQ5	iTRAQ4
iTRAQ8	iTRAQ4
iTRAQ9	iTRAQ4
itraqdata	itraqdata
lapply,MSnSetList-method	MSnSetList-class
length	pSet-class
length,Chromatogram-method	Chromatogram-class
length,FeaturesOfInterest-method	FeaturesOfInterest-class
length,FoICollection-method	FeaturesOfInterest-class
length,MSnSetList-method	MSnSetList-class
length,OnDiskMSnExp-method	OnDiskMSnExp-class
length,pSet-method	pSet-class
length,ReporterIons-method	ReporterIons-class
length-method	ReporterIons-class
lengths,FoICollection-method	FeaturesOfInterest-class
listOf	listOf
log,MSnSet-method	MSnSet-class
makeCamelCase	makeCamelCase
makeImpuritiesMatrix	purityCorrect-methods
makeMTD	defunct
makeNaData	makeNaData
makeNaData2	makeNaData
makePEP	defunct
makePRT	defunct
MAplot,MSnSet-method	MSnSet-class
MChromatograms	MChromatograms-class
MChromatograms-class	MChromatograms-class
meanMzInts	meanMzInts
meanSdPlot,MSnSet-method	MSnSet-class
mergeFeatureVars	fData-utils
metadata,MzTab-method	MzTab-class
MIAPE	MIAPE-class
MIAPE-class	MIAPE-class
missing-data	missing-data
missingdata	missing-data
moleculeEvidence	MzTab-class
moleculeFeatures	MzTab-class
ms2df	MSnSet-class
msInfo	MIAPE-class
msInfo,MIAPE-method	MIAPE-class
msInfo,MSnSet-method	MSnSet-class
msInfo,pSet-method	pSet-class
msLevel	Spectrum-class
msLevel,Chromatogram-method	Chromatogram-class
msLevel,MSmap-method	MSmap-class
msLevel,MSpectra-method	MSpectra
msLevel,OnDiskMSnExp-method	OnDiskMSnExp-class
msLevel,pSet-method	pSet-class
msLevel,Spectrum-method	Spectrum-class
MSmap	MSmap-class
msMap	MSmap-class
msMap,MSmap-method	MSmap-class
MSmap,mzRpwiz-method	MSmap-class
MSmap,mzRramp-method	MSmap-class
MSmap,mzRraw-method	MSmap-class
MSmap,OnDiskMSnExp-method	MSmap-class
MSmap-class	MSmap-class
MSmap-method	MSmap-class
MSnbase-defunct	defunct
MSnbase-deprecated	defunct
MSnbaseOptions	MSnbaseOptions
MSnExp	MSnExp-class
MSnExp-class	MSnExp-class
MSnProcess	MSnProcess-class
MSnProcess-class	MSnProcess-class
MSnSet	MSnSet-class
msnset	itraqdata
MSnSet-class	MSnSet-class
msnset2	itraqdata
MSnSetList	MSnSetList-class
MSnSetList-class	MSnSetList-class
msnsets	MSnSetList-class
MSpectra	MSpectra
MSpectra-class	MSpectra
multiLabels	defunct
multiLabels,NAnnotatedDataFrame-method	defunct
multiplex	defunct
multiplex,NAnnotatedDataFrame-method	defunct
mz	Spectrum-class
mz,Chromatogram-method	Chromatogram-class
mz,MChromatograms-method	MChromatograms-class
mz,MSmap-method	MSmap-class
mz,MSpectra-method	MSpectra
mz,OnDiskMSnExp-method	OnDiskMSnExp-class
mz,pSet-method	pSet-class
mz,ReporterIons-method	ReporterIons-class
mz,Spectrum-method	Spectrum-class
mzRes	MSmap-class
mzRes,MSmap-method	MSmap-class
MzTab	MzTab-class
MzTab-class	MzTab-class
mzTabMode	MzTab-class
mzTabType	MzTab-class
names,FeatComp-method	FeatComp-class
names,FoICollection-method	FeaturesOfInterest-class
names,MSnSetList-method	MSnSetList-class
names,ReporterIons-method	ReporterIons-class
names<-,FoICollection,character-method	FeaturesOfInterest-class
names<-,MSnSetList,ANY-method	MSnSetList-class
NAnnotatedDataFrame	defunct
NAnnotatedDataFrame-class	defunct
naplot	naplot
naset	impute
navMS	navMS
ncol,MSmap-method	MSmap-class
nextMS	navMS
nFeatures	nFeatures
normalise	normalise-methods
normalise,MSnExp-method	normalise-methods
normalise,MSnSet-method	normalise-methods
normalise,OnDiskMSnExp-method	OnDiskMSnExp-class
normalise,Spectrum-method	normalise-methods
normalise,Spectrum2-method	normalise-methods
normalise-methods	normalise-methods
normalize	normalise-methods
normalize,Chromatogram-method	Chromatogram-class
normalize,MChromatograms-method	MChromatograms-class
normalize,MSnExp-method	normalise-methods
normalize,MSnSet-method	normalise-methods
normalize,OnDiskMSnExp-method	OnDiskMSnExp-class
normalize,Spectrum-method	normalise-methods
normalize,Spectrum2-method	normalise-methods
normalize-methods	normalise-methods
normToReference	normToReference
notes,MIAPE-method	MIAPE-class
notes,pSet-method	pSet-class
notes<-,MIAPE-method	MIAPE-class
npcv	npcv
nQuants	nQuants
nrow,MSmap-method	MSmap-class
NTR	normToReference
objlog	MSnSetList-class
OnDiskMSnExp	OnDiskMSnExp-class
OnDiskMSnExp-class	OnDiskMSnExp-class
otherInfo,MIAPE-method	MIAPE-class
pData,MChromatograms-method	MChromatograms-class
pData,pSet-method	pSet-class
pData<-,MChromatograms,data.frame-method	MChromatograms-class
pData<-,MSnSet,data.frame-method	MSnSet-class
pData<-,pSet,ANY-method	pSet-class
peaksCount	Spectrum-class
peaksCount,MSpectra,ANY-method	MSpectra
peaksCount,OnDiskMSnExp,missing-method	OnDiskMSnExp-class
peaksCount,OnDiskMSnExp,numeric-method	OnDiskMSnExp-class
peaksCount,pSet,missing-method	pSet-class
peaksCount,pSet,numeric-method	pSet-class
peaksCount,Spectrum,missing-method	Spectrum-class
peptides,MzTab-method	MzTab-class
phenoData,MChromatograms-method	MChromatograms-class
phenoData,pSet-method	pSet-class
phenoData<-,pSet,ANY-method	pSet-class
pickPeaks	pickPeaks-method
pickPeaks,MSnExp-method	MSnExp-class
pickPeaks,MSpectra-method	MSpectra
pickPeaks,OnDiskMSnExp-method	OnDiskMSnExp-class
pickPeaks,Spectrum-method	Spectrum-class
pickPeaks-methods	pickPeaks-method
plot	plot-methods
plot,Chromatogram,ANY-method	Chromatogram-class
plot,MChromatograms,ANY-method	MChromatograms-class
plot,MSmap,missing-method	MSmap-class
plot,MSnExp	MSnExp-class
plot,MSnExp,missing-method	MSnExp-class
plot,Spectrum,missing-method	plot-methods
plot,Spectrum,Spectrum-method	plotSpectrumSpectrum-methods
plot,Spectrum-method	plot-methods
plot,Spectrum2,character-method	plot-methods
plot-methods	plot-methods
plot.MSnExp	plot-methods
plot.Spectrum	plot-methods
plot.Spectrum.character	plot-methods
plot.Spectrum.Spectrum	plotSpectrumSpectrum-methods
plot2d	plot2d-methods
plot2d,data.frame-method	plot2d-methods
plot2d,MSnExp-method	plot2d-methods
plot2d-methods	plot2d-methods
plot3D	MSmap-class
plot3D,MSmap-method	MSmap-class
plotDensity	plotDensity-methods
plotDensity,data.frame-method	plotDensity-methods
plotDensity,MSnExp-method	plotDensity-methods
plotDensity-methods	plotDensity-methods
plotMzDelta	plotMzDelta-methods
plotMzDelta,MSnExp-method	plotMzDelta-methods
plotMzDelta,mzRramp-method	plotMzDelta-methods
plotMzDelta-methods	plotMzDelta-methods
plotNA	plotNA-methods
plotNA,matrix-method	plotNA-methods
plotNA,MSnSet-method	plotNA-methods
plotNA-methods	plotNA-methods
polarity	Spectrum-class
polarity,MChromatograms-method	MChromatograms-class
polarity,MSpectra-method	MSpectra
polarity,OnDiskMSnExp-method	OnDiskMSnExp-class
polarity,pSet-method	pSet-class
polarity,Spectrum-method	Spectrum-class
precAcquisitionNum	Spectrum2-class
precAcquisitionNum,pSet-method	pSet-class
precAcquisitionNum,Spectrum-method	Spectrum2-class
precScanNum	Spectrum2-class
precScanNum,MSpectra-method	MSpectra
precScanNum,OnDiskMSnExp-method	OnDiskMSnExp-class
precScanNum,pSet-method	pSet-class
precScanNum,Spectrum-method	Spectrum2-class
precSelection	precSelection
precSelectionTable	precSelection
precursorCharge	Spectrum2-class
precursorCharge,MSpectra-method	MSpectra
precursorCharge,OnDiskMSnExp-method	OnDiskMSnExp-class
precursorCharge,pSet-method	pSet-class
precursorCharge,Spectrum-method	Spectrum2-class
precursorIntensity	Spectrum2-class
precursorIntensity,MSpectra-method	MSpectra
precursorIntensity,OnDiskMSnExp-method	OnDiskMSnExp-class
precursorIntensity,pSet-method	pSet-class
precursorIntensity,Spectrum-method	Spectrum2-class
precursorMz	Spectrum2-class
precursorMz,Chromatogram-method	Chromatogram-class
precursorMz,MChromatograms-method	MChromatograms-class
precursorMz,MSpectra-method	MSpectra
precursorMz,OnDiskMSnExp-method	OnDiskMSnExp-class
precursorMz,pSet-method	pSet-class
precursorMz,Spectrum-method	Spectrum2-class
prevMS	navMS
processingData	pSet-class
processingData,MSnSet-method	MSnSet-class
processingData,pSet-method	pSet-class
ProcessingStep	ProcessingStep-class
ProcessingStep-class	ProcessingStep-class
ProcessingStep:OnDiskMSnExp	ProcessingStep-class
productMz,Chromatogram-method	Chromatogram-class
productMz,MChromatograms-method	MChromatograms-class
proteins,MzTab-method	MzTab-class
protocolData,pSet-method	pSet-class
pSet	pSet-class
pSet-class	pSet-class
psms,MzTab-method	MzTab-class
pubMedIds,MIAPE-method	MIAPE-class
pubMedIds,pSet-method	pSet-class
pubMedIds<-,MIAPE-method	MIAPE-class
purityCorrect	purityCorrect-methods
purityCorrect,MSnSet,matrix-method	MSnSet-class
purityCorrect,MSnSet-method	MSnSet-class
purityCorrect-methods	purityCorrect-methods
qual	MSnSet-class
qual,MSnSet-method	MSnSet-class
quantify	quantify-methods
quantify,MSnExp,character-method	MSnExp-class
quantify,MSnExp-method	MSnExp-class
quantify,OnDiskMSnExp-method	OnDiskMSnExp-class
quantify,OnMSnExp-method	MSnExp-class
quantify,Spectrum,character-method	Spectrum-class
quantify,Spectrum-method	Spectrum-class
quantify-methods	quantify-methods
readMgfData	readMgfData
readMSData	readMSData
readMSData2	readMSData
readMSnSet	readMSnSet
readMSnSet2	readMSnSet
readMzIdData	readMzIdData
readMzTabData	readMzTabData
readMzTabData_v0.9	readMzTabData_v0.9
readMzXMLData	defunct
readSRMData	readSRMData
reduce,data.frame-method	reduce-data.frame-method
removeMultipleAssignment	MSnSet-class
removeMultipleAssignment,MSnExp-method	MSnExp-class
removeMultipleAssignment,MSnSet-method	MSnSet-class
removeMultipleAssignment-method	MSnSet-class
removeNoId	removeNoId-methods
removeNoId,MSnExp-method	MSnExp-class
removeNoId,MSnSet-method	MSnSet-class
removeNoId-methods	removeNoId-methods
removePeaks	removePeaks-methods
removePeaks,MSnExp-method	MSnExp-class
removePeaks,MSpectra-method	MSpectra
removePeaks,OnDiskMSnExp-method	OnDiskMSnExp-class
removePeaks,Spectrum-method	Spectrum-class
removePeaks-methods	removePeaks-methods
removeReporters	removeReporters-methods
removeReporters,MSnExp-method	MSnExp-class
removeReporters,OnDiskMSnExp-method	MSnExp-class
removeReporters,Spectrum-method	Spectrum2-class
removeReporters-methods	removeReporters-methods
reporterColors	ReporterIons-class
reporterColors,ReporterIons-method	ReporterIons-class
reporterColors-method	ReporterIons-class
reporterColours	ReporterIons-class
reporterColours,ReporterIons-method	ReporterIons-class
reporterColours-method	ReporterIons-class
ReporterIons	ReporterIons-class
ReporterIons-class	ReporterIons-class
reporterNames	ReporterIons-class
reporterNames,ReporterIons-method	ReporterIons-class
reporterNames-method	ReporterIons-class
reporterNames<-	ReporterIons-class
reporterNames<-,ReporterIons,ANY-method	ReporterIons-class
reporterNames<-,ReporterIons,character-method	ReporterIons-class
reporterNames<-,ReporterIons-method	ReporterIons-class
requiredFvarLabels	selectFeatureData
rmFeaturesOfInterest	FeaturesOfInterest-class
rmFeaturesOfInterest,FoICollection,numeric-method	FeaturesOfInterest-class
rmFeaturesOfInterest-methods	FeaturesOfInterest-class
rownames<-,MChromatograms-method	MChromatograms-class
rtime	Spectrum-class
rtime,Chromatogram-method	Chromatogram-class
rtime,MSmap-method	MSmap-class
rtime,MSpectra-method	MSpectra
rtime,OnDiskMSnExp-method	OnDiskMSnExp-class
rtime,pSet-method	pSet-class
rtime,Spectrum-method	Spectrum-class
sampleNames,MChromatograms-method	MChromatograms-class
sampleNames,pSet-method	pSet-class
sampleNames<-,MChromatograms,ANY-method	MChromatograms-class
sampleNames<-,pSet,character-method	pSet-class
samples,MIAPE-method	MIAPE-class
sapply,MSnSetList-method	MSnSetList-class
scale,MSnSet-method	normalise-methods
scanIndex	Spectrum-class
scanIndex,MSpectra-method	MSpectra
scanIndex,OnDiskMSnExp-method	OnDiskMSnExp-class
scanIndex,pSet-method	pSet-class
scanIndex,Spectrum-method	Spectrum-class
selectFeatureData	selectFeatureData
setMSnbaseFastLoad	MSnbaseOptions
setMSnbaseParallelThresh	MSnbaseOptions
setMSnbaseVerbose	MSnbaseOptions
show,Chromatogram-method	Chromatogram-class
show,FeatComp-method	FeatComp-class
show,FeaturesOfInterest-method	FeaturesOfInterest-class
show,FoICollection-method	FeaturesOfInterest-class
show,MChromatograms-method	MChromatograms-class
show,MIAPE-method	MIAPE-class
show,MSmap-method	MSmap-class
show,MSnExp-method	MSnExp-class
show,MSnProcess-method	MSnProcess-class
show,MSnSet-method	MSnSet-class
show,MSnSetList-method	MSnSetList-class
show,MSpectra-method	MSpectra
show,MzTab-method	MzTab-class
show,NAnnotatedDataFrame-method	defunct
show,OnDiskMSnExp-method	OnDiskMSnExp-class
show,ProcessingStep-method	ProcessingStep-class
show,ReporterIons-method	ReporterIons-class
show,Spectrum-method	Spectrum-class
smallMolecules	MzTab-class
smooth	smooth-methods
smooth,MSnExp-method	MSnExp-class
smooth,MSpectra-method	MSpectra
smooth,OnDiskMSnExp-method	OnDiskMSnExp-class
smooth,Spectrum-method	Spectrum-class
smooth-methods	smooth-methods
smoothed	Spectrum-class
smoothed,MSpectra-method	MSpectra
smoothed,OnDiskMSnExp-method	OnDiskMSnExp-class
smoothed,pSet-method	pSet-class
smoothed,Spectrum-method	Spectrum-class
smoothed<-	Spectrum-class
smoothed<-,OnDiskMSnExp,logical-method	OnDiskMSnExp-class
smoothed<-,pSet,ANY-method	pSet-class
smoothed<-,pSet,logical-method	pSet-class
smoothed<-,Spectrum,ANY-method	Spectrum-class
smoothed<-,Spectrum,logical-method	Spectrum-class
spectra	pSet-class
spectra,MSnExp-method	MSnExp-class
spectra,OnDiskMSnExp-method	OnDiskMSnExp-class
spectra,pSet-method	pSet-class
spectrapply	pSet-class
spectrapply,OnDiskMSnExp-method	OnDiskMSnExp-class
spectrapply,pSet-method	pSet-class
Spectrum	Spectrum-class
Spectrum-class	Spectrum-class
Spectrum1	Spectrum1-class
Spectrum1-class	Spectrum1-class
Spectrum2	Spectrum2-class
Spectrum2-class	Spectrum2-class
split,MSnSet,character-method	MSnSetList-class
split,MSnSet,factor-method	MSnSetList-class
splitByFile	MSnExp-class
splitByFile,MSnExp,factor-method	MSnExp-class
splitByFile,OnDiskMSnExp,factor-method	MSnExp-class
t,MSmap-method	MSmap-class
t.MSnSet	MSnSet-class
tic	Spectrum-class
tic,MSpectra-method	MSpectra
tic,OnDiskMSnExp-method	OnDiskMSnExp-class
tic,pSet-method	pSet-class
tic,Spectrum-method	Spectrum-class
TMT10	TMT6
TMT10ETD	TMT6
TMT10HCD	TMT6
TMT11	TMT6
TMT11HCD	TMT6
TMT16	TMT6
TMT16HCD	TMT6
TMT6	TMT6
TMT6b	TMT6
TMT7	TMT6
TMT7b	TMT6
topN	MSnSet-class
topN,matrix-method	MSnSet-class
topN,MSnSet,MSnSet-method	MSnSet-class
topN,MSnSet-method	MSnSet-class
transformIntensity	Chromatogram-class
transformIntensity,Chromatogram-method	Chromatogram-class
transformIntensity,MChromatograms-method	MChromatograms-class
trimMz	trimMz-methods
trimMz,MSnExp,numeric-method	MSnExp-class
trimMz,MSnExp-method	MSnExp-class
trimMz,OnDiskMSnExp,numeric-method	OnDiskMSnExp-class
trimMz,Spectrum,numeric-method	Spectrum-class
trimMz,Spectrum-method	Spectrum-class
trimMz-methods	trimMz-methods
trimws	MSnSet-class
trimws,data.frame-method	MSnSet-class
trimws,MSnSet-method	MSnSet-class
unique1	FeatComp-class
unique1,FeatComp-method	FeatComp-class
unique1,methods	FeatComp-class
unique2	FeatComp-class
unique2,FeatComp-method	FeatComp-class
unique2,methods	FeatComp-class
unsplit,MSnSetList,factor-method	MSnSetList-class
updateFeatureNames	MSnSet-class
updateFvarLabels	MSnSet-class
updateObject,MSnExp-method	updateObject-methods
updateObject,Spectrum-method	updateObject-methods
updateSampleNames	MSnSet-class
validateOnDiskMSnExp	OnDiskMSnExp-class
varLabels,pSet-method	pSet-class
varMetadata,pSet-method	pSet-class
whichNA	makeNaData
width	ReporterIons-class
width,ReporterIons-method	ReporterIons-class
width-method	ReporterIons-class
write.exprs	MSnSet-class
write.exprs,MSnSet-method	MSnSet-class
writeMgfData	writeMgfData-methods
writeMgfData,MSnExp-method	writeMgfData-methods
writeMgfData,MSpectra-method	MSpectra
writeMgfData,Spectrum-method	writeMgfData-methods
writeMgfData-methods	writeMgfData-methods
writeMSData	writeMSData
writeMSData,MSnExp,character-method	writeMSData
writeMzTabData	writeMzTabData
[,FoICollection,ANY,ANY,ANY-method	FeaturesOfInterest-class
[,FoICollection,ANY,ANY-method	FeaturesOfInterest-class
[,FoICollection-method	FeaturesOfInterest-class
[,MChromatograms,ANY,ANY,ANY-method	MChromatograms-class
[,MSnSet,ANY,ANY,ANY-method	MSnSet-class
[,MSnSet,ANY,ANY-method	MSnSet-class
[,MSnSet-method	MSnSet-class
[,MSnSetList,ANY,ANY,ANY-method	MSnSetList-class
[,MSnSetList,ANY,missing,missing-method	MSnSetList-class
[,OnDiskMSnExp,ANY,ANY,ANY-method	OnDiskMSnExp-class
[,OnDiskMSnExp,logicalOrNumeric,missing,missing-method	OnDiskMSnExp-class
[,pSet,ANY,ANY,ANY-method	pSet-class
[,pSet,ANY,ANY-method	pSet-class
[,pSet-method	pSet-class
[,ReporterIons,ANY,ANY,ANY-method	ReporterIons-class
[,ReporterIons,ANY,ANY-method	ReporterIons-class
[,ReporterIons-method	ReporterIons-class
[<-,MChromatograms-method	MChromatograms-class
[[,FoICollection,ANY,ANY-method	FeaturesOfInterest-class
[[,FoICollection-method	FeaturesOfInterest-class
[[,MSnSetList,ANY,ANY-method	MSnSetList-class
[[,MSnSetList,ANY,missing-method	MSnSetList-class
[[,OnDiskMSnExp,ANY,ANY,missing-method	OnDiskMSnExp-class
[[,OnDiskMSnExp,ANY,ANY-method	OnDiskMSnExp-class
[[,OnDiskMSnExp,ANY,missing,missing-method	OnDiskMSnExp-class
[[,OnDiskMSnExp-method	OnDiskMSnExp-class
[[,pSet,ANY,ANY-method	pSet-class
[[,pSet-method	pSet-class
