# Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching

## Documentation for package ‘IPPD’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

IPPD-package | Peak pattern deconvolution for Protein Mass Spectrometry by non-negative ls/lad template matching
analyzeLCMS | Functionality for LC-MS data
calculatebasis.emg | Internal functions
calculatebasis.gaussian | Internal functions
calculatedenoisingbasis.emg | Internal functions
calculatedenoisingbasis.gaussian | Internal functions
dalpha | Internal functions
determinemode | Internal functions
dmu | Internal functions
dsigma | Internal functions
EMG | Internal functions
erfc | Internal functions
examples_boxes | Internal functions
fit.combine | Internal functions
fit.EMG | Internal functions
fit.gauss | Internal functions
fitModelParameters | Peak parameter estimation
fitModelParameters-method | Peak parameter estimation
fitModelParameters-methods | Peak parameter estimation
formulacoef2function | Internal functions
gaussfun | Internal functions
getpeakheights | Internal functions
getPeaklist | Peak pattern extraction by non-negative ls/lad template matching
getPeaklist-method | Peak pattern extraction by non-negative ls/lad template matching
getPeaklist-methods | Peak pattern extraction by non-negative ls/lad template matching
grad | Internal functions
grad.combine | Internal functions
gridsearch | Internal functions
intermediate.gaussian | Internal functions
intermediateemg | Internal functions
linesearch | Internal functions
linesearchlad | Internal functions
localnoise | Internal functions
modelfit | "Modelfit"
modelfit-class | "Modelfit"
myo500 | Myoglobine dataset
new.mzXML | Import of data in mzXML format
nnladlogbarrier | Internal functions
nnlslogbarrier | Internal functions
objective | Internal functions
objective.combine | Internal functions
P1 | Internal functions
P2 | Internal functions
P3 | Internal functions
P3prime | Internal functions
peakdetect | Internal functions
peaklist | "Peaklist"
peaklist-class | "Peaklist"
postprocess.emg | Internal functions
postprocess.gaussian | Internal functions
read.mzXML | Import of data in mzXML format
show-method | "Modelfit"
show-method | "Peaklist"
simplepeakdetect | Internal functions
sweepline | Sweep line scheme to process LC-MS data
tableaveragine | Internal functions
threshold | "Peaklist"
threshold-method | "Peaklist"
toyspectrum | Simulated protein mass spectrum
toyspectrumsolution | Simulated protein mass spectrum
visualize | "Peaklist"
visualize-method | "Modelfit"
visualize-method | "Peaklist"