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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.
Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data.
This is an R package for the Mass spectrometry Research. The MrR can be used to analyze the mass spectrometry data for baseline correction, denoising, peak detection, peak alignment, peak normalization, and biomarker discovery.
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Peakplot is a Perl implemented freely available software application which labels peptide tandem mass spectra retrospectively after a Mascot database search.
Availability: http://fgcz-peakplot.uzh.ch/
We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.
m0n0merhunter is a command line program for computing the most frequent delta masses of ultra high mass resolution and accurate mass measurements using mass spectrometer data.