Quantitative Analysis of Mass Spectrometry Data
Quantitative Analysis of Mass Spectrometry Data
Parallel Support in Package MALDIquant
Class "AbstractMassObject"
Align MassSpectrum objects.
Averages MassSpectrum objects.
Align Peaks into discrete bins.
Calibrates intensities of a MassSpectrum object.
Creates a MassPeaks object.
Creates a MassSpectrum object.
Detects peaks in a MassSpectrum object.
Determine warping functions of MassPeaks objects.
Estimates the baseline of a MassSpectrum object.
Estimates the noise of a MassSpectrum object.
Removes less frequent peaks.
Finds or removes empty AbstractMassObject objects in a list.
Converts a list of MassPeaks objects into a matrix.
Tests for MassSpectrum or MassPeaks object.
Tests a list of MassSpectrum or MassPeaks objects.
Draws peak labels to plot.
Removed Functions/Methods in Package MALDIquant
Deprecated Functions/Methods in Package MALDIquant
Class "MassPeaks"
Class "MassSpectrum"
Relaxed Value Matching
Merges MassPeaks objects.
Finds monoisotopic peaks in a MassPeaks object.
Turn a list of AbstractMassObjects into a mass spectrometry imaging sl...
Plots an AbstractMassObject object.
Plots a Mass Spectrometry Imaging dataset.
Creates a reference MassPeaks object.
Removes the baseline of a MassSpectrum object.
Smoothes intensities of a MassSpectrum object.
Transforms intensities of an AbstractMassObject object.
Trim an AbstractMassObject object.
Run warping functions on AbstractMassObject objects.
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Useful links