MSnbase-package	MSnbase-package
abstract,MIAPE-method	MIAPE-class
abstract,pSet-method	pSet-class
acquisitionNum	Spectrum-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,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-methods	addIdentificationData-methods
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.data.frame.MSnSet	MSnSet-class
as.data.frame.Spectrum	Spectrum-class
as.ExpressionSet.MSnSet	MSnSet-class
as.MIAME.MIAPE	MIAPE-class
as.MSnSet.ExpressionSet	MSnSet-class
assayData,pSet-method	pSet-class
averageMSnSet	averageMSnSet
bin	bin-methods
bin,MSnExp-method	MSnExp-class
bin,Spectrum-method	Spectrum-class
bin-methods	bin-methods
calculateFragments	calculateFragments-methods
calculateFragments,character,missing-method	calculateFragments-methods
calculateFragments,character,Spectrum2-method	Spectrum2-class
centroided	Spectrum-class
centroided,pSet-method	pSet-class
centroided,Spectrum-method	Spectrum-class
centroided<-	Spectrum-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-methods
chromatogram,character-method	chromatogram-methods
chromatogram,data.frame-method	chromatogram-methods
chromatogram,mzRramp-method	chromatogram-methods
chromatogram-methods	chromatogram-methods
class:MIAPE	MIAPE-class
class:MSnExp	MSnExp-class
class:MSnProcess	MSnProcess-class
class:MSnSet	MSnSet-class
class:NAnnotatedDataFrame	NAnnotatedDataFrame-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,MSnExp-method	MSnExp-class
clean,Spectrum-method	Spectrum-class
clean-methods	clean-methods
coerce,ExpressionSet,MSnSet-method	MSnSet-class
coerce,MIAPE,MIAME-method	MIAPE-class
coerce,MSmap,data.frame-method	MSmap-class
coerce,MSnSet,data.frame-method	MSnSet-class
coerce,MSnSet,ExpressionSet-method	MSnSet-class
coerce,Spectrum,data.frame-method	Spectrum-class
collisionEnergy	Spectrum2-class
collisionEnergy,pSet-method	pSet-class
collisionEnergy,Spectrum-method	Spectrum2-class
combine,MIAPE,MIAPE-method	MIAPE-class
combine,MSnProcess,MSnProcess-method	MSnProcess-class
combine,MSnSet,MSnSet-method	MSnSet-class
combineFeatures	combineFeatures
common	FeatComp-class
common,FeatComp-method	FeatComp-class
common,methods	FeatComp-class
compareSpectra	compareSpectra-methods
compareSpectra,MSnExp,missing-method	MSnExp-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
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	NAnnotatedDataFrame-class
dim,pSet-method	pSet-class
droplevels.MSnSet	MSnSet-class
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
exprsToRatios	exprsToRatios-methods
exprsToRatios,matrix-method	exprsToRatios-methods
exprsToRatios,MSnSet-method	exprsToRatios-methods
exprsToRatios-methods	exprsToRatios-methods
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-methods	extractPrecSpectra-methods
fData,pSet-method	pSet-class
fData<-,pSet,data.frame-method	pSet-class
FeatComp-class	FeatComp-class
featureCV	featureCV
featureData,pSet-method	pSet-class
featureNames,pSet-method	pSet-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
fileNames	pSet-class
fileNames,MSnProcess-method	MSnProcess-class
fileNames,MSnSet-method	MSnSet-class
fileNames,pSet-method	pSet-class
fillUp	fillUp
filterNA	MSnSet-class
filterNA,matrix-method	MSnSet-class
filterNA,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,pSet-method	pSet-class
fromFile,Spectrum-method	Spectrum-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
getRatios	exprsToRatios-methods
getVariableName	getVariableName
grepEcols	grepEcols
header	pSet-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
imageNA2	imageNA2
impute	impute-methods
impute,MSnSet-method	impute-methods
impute-methods	impute-methods
imputeMethods	impute-methods
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,pSet-method	pSet-class
intensity,Spectrum-method	Spectrum-class
ionCount	Spectrum-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
is.na.MSnSet	plotNA-methods
isEmpty,Spectrum-method	Spectrum-class
iTRAQ4	iTRAQ4
iTRAQ5	iTRAQ4
iTRAQ8	iTRAQ4
iTRAQ9	iTRAQ4
itraqdata	itraqdata
length	pSet-class
length,FeaturesOfInterest-method	FeaturesOfInterest-class
length,FoICollection-method	FeaturesOfInterest-class
length,pSet-method	pSet-class
length,ReporterIons-method	ReporterIons-class
length-method	ReporterIons-class
listOf	listOf
log,MSnSet-method	MSnSet-class
makeImpuritiesMatrix	purityCorrect-methods
makeMTD	makeMTD
makePEP	makePEP
makePRT	makePRT
MAplot,MSnSet-method	MSnSet-class
meanSdPlot,MSnSet-method	MSnSet-class
MIAPE	MIAPE-class
MIAPE-class	MIAPE-class
missing-data	missing-data
missingdata	missing-data
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,MSmap-method	MSmap-class
msLevel,pSet-method	pSet-class
msLevel,Spectrum-method	Spectrum-class
MSmap	MSmap-class
msMap	MSmap-class
msMap,MSmap-method	MSmap-class
MSmap-class	MSmap-class
MSnbase	MSnbase-package
MSnbase-defunct	defunct
MSnbase-deprecated	defunct
MSnExp	MSnExp-class
MSnExp-class	MSnExp-class
MSnProcess	MSnProcess-class
MSnProcess-class	MSnProcess-class
MSnSet	MSnSet-class
msnset	itraqdata
MSnSet-class	MSnSet-class
multiLabels	NAnnotatedDataFrame-class
multiLabels,NAnnotatedDataFrame-method	NAnnotatedDataFrame-class
multiplex	NAnnotatedDataFrame-class
multiplex,NAnnotatedDataFrame-method	NAnnotatedDataFrame-class
mz	Spectrum-class
mz,MSmap-method	MSmap-class
mz,pSet-method	pSet-class
mz,ReporterIons-method	ReporterIons-class
mz,Spectrum-method	Spectrum-class
mzRes	MSmap-class
mzRes,MSmap-method	MSmap-class
names,FeatComp-method	FeatComp-class
names,ReporterIons-method	ReporterIons-class
NAnnotatedDataFrame	NAnnotatedDataFrame-class
NAnnotatedDataFrame-class	NAnnotatedDataFrame-class
naset	impute-methods
ncol,MSmap-method	MSmap-class
normalise	normalise-methods
normalise,MSnExp-method	normalise-methods
normalise,MSnSet-method	normalise-methods
normalise,Spectrum-method	normalise-methods
normalise,Spectrum2-method	normalise-methods
normalise-methods	normalise-methods
normalize	normalise-methods
normalize,MSnExp-method	normalise-methods
normalize,MSnSet-method	normalise-methods
normalize,Spectrum-method	normalise-methods
normalize,Spectrum2-method	normalise-methods
normalize-methods	normalise-methods
notes,MIAPE-method	MIAPE-class
notes,pSet-method	pSet-class
notes<-,MIAPE-method	MIAPE-class
npcv	npcv
nQuants	nQuants
nrow,MSmap-method	MSmap-class
otherInfo,MIAPE-method	MIAPE-class
pData,pSet-method	pSet-class
peaksCount	Spectrum-class
peaksCount,pSet,missing-method	pSet-class
peaksCount,pSet,numeric-method	pSet-class
peaksCount,Spectrum,missing-method	Spectrum-class
phenoData,pSet-method	pSet-class
pickPeaks	pickPeaks-method
pickPeaks,MSnExp-method	MSnExp-class
pickPeaks,Spectrum-method	Spectrum-class
pickPeaks-methods	pickPeaks-method
plot	plot-methods
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	Spectrum1-class
polarity,pSet-method	pSet-class
polarity,Spectrum-method	Spectrum1-class
precAcquisitionNum	Spectrum2-class
precAcquisitionNum,pSet-method	pSet-class
precAcquisitionNum,Spectrum-method	Spectrum2-class
precScanNum	Spectrum2-class
precScanNum,pSet-method	pSet-class
precScanNum,Spectrum-method	Spectrum2-class
precSelection	precSelection
precSelectionTable	precSelection
precursorCharge	Spectrum2-class
precursorCharge,pSet-method	pSet-class
precursorCharge,Spectrum-method	Spectrum2-class
precursorIntensity	Spectrum2-class
precursorIntensity,pSet-method	pSet-class
precursorIntensity,Spectrum-method	Spectrum2-class
precursorMz	Spectrum2-class
precursorMz,pSet-method	pSet-class
precursorMz,Spectrum-method	Spectrum2-class
processingData	pSet-class
processingData,MSnSet-method	MSnSet-class
processingData,pSet-method	pSet-class
protocolData,pSet-method	pSet-class
pSet	pSet-class
pSet-class	pSet-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,Spectrum,character-method	Spectrum-class
quantify,Spectrum-method	Spectrum-class
quantify-methods	quantify-methods
readIspyData	readIspyData
readMgfData	readMgfData
readMSData	readMSData
readMSnSet	readMSnSet
readMSnSet2	readMSnSet
readMzTabData	readMzTabData
readMzXMLData	defunct
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,Spectrum-method	Spectrum-class
removePeaks-methods	removePeaks-methods
removeReporters	removeReporters-methods
removeReporters,MSnExp-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
rmFeaturesOfInterest	FeaturesOfInterest-class
rmFeaturesOfInterest,FoICollection,numeric-method	FeaturesOfInterest-class
rmFeaturesOfInterest-methods	FeaturesOfInterest-class
rtime	Spectrum-class
rtime,MSmap-method	MSmap-class
rtime,pSet-method	pSet-class
rtime,Spectrum-method	Spectrum-class
sampleNames,pSet-method	pSet-class
samples,MIAPE-method	MIAPE-class
scale,MSnSet-method	normalise-methods
scanIndex	Spectrum-class
scanIndex,pSet-method	pSet-class
scanIndex,Spectrum-method	Spectrum-class
show,FeatComp-method	FeatComp-class
show,FeaturesOfInterest-method	FeaturesOfInterest-class
show,FoICollection-method	FeaturesOfInterest-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,NAnnotatedDataFrame-method	NAnnotatedDataFrame-class
show,ReporterIons-method	ReporterIons-class
show,Spectrum-method	Spectrum-class
smooth	smooth-methods
smooth,MSnExp-method	MSnExp-class
smooth,Spectrum-method	Spectrum-class
smooth-methods	smooth-methods
spectra	pSet-class
spectra,MSnExp-method	MSnExp-class
spectra,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
t,MSmap-method	MSmap-class
t.MSnSet	MSnSet-class
tic	Spectrum-class
tic,pSet-method	pSet-class
tic,Spectrum-method	Spectrum-class
TMT10	TMT6
TMT6	TMT6
TMT7	TMT6
topN	MSnSet-class
topN,matrix-method	MSnSet-class
topN,MSnSet,MSnSet-method	MSnSet-class
topN,MSnSet-method	MSnSet-class
trimMz	trimMz-methods
trimMz,MSnExp,numeric-method	MSnExp-class
trimMz,MSnExp-method	MSnExp-class
trimMz,Spectrum,numeric-method	Spectrum-class
trimMz,Spectrum-method	Spectrum-class
trimMz-methods	trimMz-methods
unique1	FeatComp-class
unique1,FeatComp-method	FeatComp-class
unique1,methods	FeatComp-class
unique2	FeatComp-class
unique2,FeatComp-method	FeatComp-class
unique2,methods	FeatComp-class
updateFeatureNames	MSnSet-class
updateFvarLabels	MSnSet-class
updateSampleNames	MSnSet-class
varLabels,pSet-method	pSet-class
varMetadata,pSet-method	pSet-class
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,Spectrum-method	writeMgfData-methods
writeMgfData-methods	writeMgfData-methods
writeMzTabData	writeMzTabData
xic	xic-methods
xic,character-method	xic-methods
xic,mzRramp-method	xic-methods
xic-methods	xic-methods
[,MSnSet,ANY,ANY,ANY-method	MSnSet-class
[,MSnSet,ANY,ANY-method	MSnSet-class
[,MSnSet-method	MSnSet-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
[[,pSet,ANY,ANY-method	pSet-class
[[,pSet-method	pSet-class
