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

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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.

Author
Martin 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 publication
None
Maintainer
Martin Slawski <ms@cs.uni-saarland.de>
License
GPL (version 2 or later)
Version
1.22.0

View on Bioconductor

Man pages

analyzeLCMS
Functionality for LC-MS data
fitModelParameters
Peak parameter estimation
getPeaklist
Peak pattern extraction by non-negative ls/lad template...
internals
Internal functions
IPPD-package
Peak pattern deconvolution for Protein Mass Spectrometry by...
modelfit-class
"Modelfit"
myo500
Myoglobine dataset
peaklist-class
"Peaklist"
read.mzXML
Import of data in mzXML format
sweepline
Sweep line scheme to process LC-MS data
toyspectrum
Simulated protein mass spectrum

Files in this package

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