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
assayData,pSet-method	pSet-class
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
collisionEnergy	Spectrum2-class
collisionEnergy,pSet-method	pSet-class
collisionEnergy,Spectrum-method	Spectrum2-class
description,pSet-method	pSet-class
dim	pSet-class
dim,MSnSet-method	MSnSet-class
dim,NAnnotatedDataFrame-method	NAnnotatedDataFrame-class
dim,pSet-method	pSet-class
experimentData,pSet-method	pSet-class
expinfo,MIAPE-method	MIAPE-class
extractPrecSpectra	extractPrecSpectra-methods
extractPrecSpectra,MSnExp,numeric-method	MSnExp-class
extractPrecSpectra,MSnExp-method	MSnExp-class
extractPrecSpectra-methods	extractPrecSpectra-methods
extractSpectra	extractSpectra-methods
extractSpectra,MSnExp,logical-method	MSnExp-class
extractSpectra,MSnExp-method	MSnExp-class
extractSpectra-methods	extractSpectra-methods
fData,pSet-method	pSet-class
featureData,pSet-method	pSet-class
featureNames,pSet-method	pSet-class
fileNames	pSet-class
fileNames,MSnProcess-method	MSnProcess-class
fileNames,MSnSet-method	MSnSet-class
fileNames,pSet-method	pSet-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
header	pSet-class
header,pSet-method	pSet-class
intensity	Spectrum-class
intensity,pSet-method	pSet-class
intensity,Spectrum-method	Spectrum-class
iTRAQ4	iTRAQ4
iTRAQ5	iTRAQ4
iTRAQ8	iTRAQ4
iTRAQ9	iTRAQ4
length	pSet-class
length,pSet-method	pSet-class
length,ReporterIons-method	ReporterIons-class
length-method	ReporterIons-class
MIAPE	MIAPE-class
MIAPE-class	MIAPE-class
msInfo	MIAPE-class
msInfo,MIAPE-method	MIAPE-class
msInfo,MSnSet-method	MSnSet-class
msInfo,pSet-method	pSet-class
msLevel	Spectrum-class
msLevel,pSet-method	pSet-class
msLevel,Spectrum-method	Spectrum-class
MSnbase	MSnbase-package
MSnExp	MSnExp-class
MSnExp-class	MSnExp-class
MSnProcess	MSnProcess-class
MSnProcess-class	MSnProcess-class
MSnSet	MSnSet-class
MSnSet-class	MSnSet-class
multiLabels	NAnnotatedDataFrame-class
multiLabels,NAnnotatedDataFrame-method	NAnnotatedDataFrame-class
multiplex	NAnnotatedDataFrame-class
multiplex,NAnnotatedDataFrame-method	NAnnotatedDataFrame-class
mz	Spectrum-class
mz,pSet-method	pSet-class
mz,ReporterIons-method	ReporterIons-class
mz,Spectrum-method	Spectrum-class
mz-method	ReporterIons-class
NAnnotatedDataFrame	NAnnotatedDataFrame-class
NAnnotatedDataFrame-class	NAnnotatedDataFrame-class
notes,MIAPE-method	MIAPE-class
notes,pSet-method	pSet-class
notes<-,MIAPE-method	MIAPE-class
otherInfo,MIAPE-method	MIAPE-class
pData,pSet-method	pSet-class
peaksCount	Spectrum-class
peaksCount,pSet-method	pSet-class
peaksCount,Spectrum-method	Spectrum-class
phenoData,pSet-method	pSet-class
plot	plot-methods
plot,MSnExp	MSnExp-class
plot,MSnExp,missing-method	MSnExp-class
plot,Spectrum,missing-method	Spectrum-class
plot,Spectrum-method	Spectrum-class
plot-methods	plot-methods
plot.MSnExp	plot-methods
plot.Spectrum	plot-methods
plot2d	plot2d-methods
plot2d,data.frame,character-method	plot2d-methods
plot2d,MSnExp,character-method	MSnExp-class
plot2d,MSnExp-method	MSnExp-class
plot2d-methods	plot2d-methods
polarity	Spectrum1-class
polarity,pSet-method	pSet-class
polarity,Spectrum-method	Spectrum1-class
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
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
readMzXMLData	readMzXMLData
removePeaks	removePeaks-methods
removePeaks,MSnExp-method	MSnExp-class
removePeaks,Spectrum-method	Spectrum-class
removePeaks-methods	removePeaks-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
rtime	Spectrum-class
rtime,pSet-method	pSet-class
rtime,Spectrum-method	Spectrum-class
sampleNames,pSet-method	pSet-class
samples,MIAPE-method	MIAPE-class
show,MIAPE-method	MIAPE-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
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
tic	Spectrum-class
tic,pSet-method	pSet-class
tic,Spectrum-method	Spectrum-class
TMT6	TMT6
TMT7	TMT6
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
varLabels,pSet-method	pSet-class
varMetadata,pSet-method	pSet-class
width	ReporterIons-class
width,ReporterIons-method	ReporterIons-class
width-method	ReporterIons-class
[,pSet-method	pSet-class
[,ReporterIons-method	ReporterIons-class
[[,pSet-method	pSet-class
