IPPD: Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching

The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.

AuthorMartin Slawski <ms@cs.uni-saarland.de>, Rene Hussong <rene.hussong@uni.lu>, Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de>, Matthias Hein <hein@cs.uni-saarland.de>
Date of publicationNone
MaintainerMartin Slawski <ms@cs.uni-saarland.de>
LicenseGPL (version 2 or later)
Version1.22.0

View on Bioconductor

Functions

analyzeLCMS Man page
calculatebasis.emg Man page
calculatebasis.gaussian Man page
calculatedenoisingbasis.emg Man page
calculatedenoisingbasis.gaussian Man page
dalpha Man page
determinemode Man page
dmu Man page
dsigma Man page
EMG Man page
erfc Man page
examples_boxes Man page
fit.combine Man page
fit.EMG Man page
fit.gauss Man page
fitModelParameters Man page
fitModelParameters-methods Man page
fitModelParameters,numeric,numeric-method Man page
formulacoef2function Man page
gaussfun Man page
getpeakheights Man page
getPeaklist Man page
getPeaklist-methods Man page
getPeaklist,numeric,numeric-method Man page
grad Man page
grad.combine Man page
gridsearch Man page
intermediateemg Man page
intermediate.gaussian Man page
IPPD-package Man page
linesearch Man page
linesearchlad Man page
localnoise Man page
modelfit Man page
modelfit-class Man page
myo500 Man page
new.mzXML Man page
nnladlogbarrier Man page
nnlslogbarrier Man page
objective Man page
objective.combine Man page
P1 Man page
P2 Man page
P3 Man page
P3prime Man page
peakdetect Man page
peaklist Man page
peaklist-class Man page
postprocess.emg Man page
postprocess.gaussian Man page
read.mzXML Man page
show,modelfit-method Man page
show,peaklist-method Man page
simplepeakdetect Man page
sweepline Man page
tableaveragine Man page
threshold Man page
threshold,peaklist-method Man page
toyspectrum Man page
toyspectrumsolution Man page
visualize Man page
visualize,modelfit,missing,missing-method Man page
visualize,peaklist,numeric,numeric-method Man page

Files

IPPD/DESCRIPTION
IPPD/NAMESPACE
IPPD/R
IPPD/R/analyzeLCMS.R IPPD/R/classes.R IPPD/R/fitModelParameters.R IPPD/R/getPeaklist.R IPPD/R/internals.R IPPD/R/methods.R IPPD/R/read.mzXML.R IPPD/R/sweepline.R
IPPD/build
IPPD/build/vignette.rds
IPPD/data
IPPD/data/examples_boxes.txt
IPPD/data/myo500.rda
IPPD/data/tableaveragine.rda
IPPD/data/toyspectrum.rda
IPPD/data/toyspectrumsolution.rda
IPPD/inst
IPPD/inst/doc
IPPD/inst/doc/IPPD.R
IPPD/inst/doc/IPPD.Rnw
IPPD/inst/doc/IPPD.pdf
IPPD/inst/news
IPPD/man
IPPD/man/IPPD-package.Rd IPPD/man/analyzeLCMS.Rd IPPD/man/fitModelParameters.Rd IPPD/man/getPeaklist.Rd IPPD/man/internals.Rd IPPD/man/modelfit-class.Rd IPPD/man/myo500.Rd IPPD/man/peaklist-class.Rd IPPD/man/read.mzXML.Rd IPPD/man/sweepline.Rd IPPD/man/toyspectrum.Rd
IPPD/src
IPPD/src/R_init_IPPD.c
IPPD/src/addiagonal.h
IPPD/src/emgbasis.h
IPPD/src/gaussbasis.h
IPPD/src/generatebinning.h
IPPD/src/gridsearchemg.h
IPPD/src/interpolatepeakheights.h
IPPD/src/localquantile.h
IPPD/src/multiply.h
IPPD/src/mzfilter.h
IPPD/src/peakdetect.h
IPPD/vignettes
IPPD/vignettes/IPPD.Rnw
IPPD/vignettes/lcms.jpg
IPPD/vignettes/preamble_paper.tex
IPPD/vignettes/references.bib
IPPD/vignettes/templatedetail.pdf
IPPD/vignettes/templates.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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