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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("IPPD")
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>
Bioconductor views Proteomics
Date of publicationNone
MaintainerMartin Slawski <ms@cs.uni-saarland.de>
LicenseGPL (version 2 or later)
Version1.24.0

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

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

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