AA	AA
aa2mass	aa2mass
apex	fetuinLFQ
as.data.frame.fragmentIonSet	fragmentIons
as.data.frame.mascot	mascot
as.data.frame.psmSet	psm
as.psm.mascot_query	mascot
as.psmSet	psmSet
as.psmSet.mascot	psmSet
averagine	averagine
bymatrix	fragmentIons
defaultIon	fragmentIons
deisotoper	deisotoper
de_novo	de_novo
empai	fetuinLFQ
FASTA	fasta
Fasta	fasta
fasta	fasta
fetuinLFQ	fetuinLFQ
findMz	PTM_MarkerFinder
findMz.mascot	PTM_MarkerFinder
findMz.psmSet	PTM_MarkerFinder
findNN	findNN
findNN_	findNN
fragmentIon	fragmentIons
genMod	genMod
HexNAc	HexNAc
hydrophobicity	ssrc
ionseries	fragmentIons
iRT	iRTpeptides
irt	iRTpeptides
iRTpeptides	iRTpeptides
is.mascot	mascot
is.mascot_query	mascot
is.psm	psm
is.psmSet	psmSet
iTRAQ	iTRAQ
iTRAQ2GroupAnalysis	iTRAQ2GroupAnalysis
lcmsmap	lcmsmap
lcmsoverview	lcmsmap
lower_bound_	findNN
mascot	mascot
massDeviationPlot	mdp
mdp	mdp
msms	msms
NN	findNN
parentIonMass	parentIonMass
peakplot	peakplot
peakplot.label	peakplot
peakplot.pie	peakplot
peakplot.putlabel	peakplot
pep3d	lcmsmap
pepmass	parentIonMass
pgImporter	pgImporter
pgLFQaov	pgLFQaov
pgLFQfeature	pgLFQfeature
pgLFQprot	pgLFQprot
pgLFQtNpq	pgLFQtNpq
pim	parentIonMass
plot.mascot	mascot
plot.mascot_query	mascot
plot.psm	peakplot
plot.psmSet	lcmsmap
ppp	ppp
pps	pps
pPTM	PTM_MarkerFinder
pressureProfile	pressureProfile
pressureProfilePlot	ppp
pressureProfileSummary	pps
protViz	peakplot
psm	psm
PTM_MarkerFinder	PTM_MarkerFinder
PTM_MarkerFinder_util	PTM_MarkerFinder_util
ssrc	ssrc
summary.mascot	mascot
summary.psmSet	psm
t3pq	fetuinLFQ
tNpq	pgLFQtNpq
