lc-ms

BatMass: mass-spec data visualization
A framework for LC-MS data visualization and exploration. View spectra, extracted ion chromatograms and 2D ion maps of LC-MS experiments. Synchronized viewers.
batmass.org Demo video Code Manuscript
BatMass: mass-spec data visualization
MSFTBX: MS File Toolbox
A fast Java library for mass spectrometry data files access (mzML, mzXML, pepXML, protXML, mzId, mzIdentML, etc). Writers for some formats are also available. Available on Maven Central.
Maven Central GitHub Manuscript
MSFTBX: MS File Toolbox
FragPipe: Proteomics 0-60 in 5 seconds
A cross-platform pipeline for comprehensive analysis of LC/MS proteomics data. Graphical User Interface (GUI) for running MSFragger (search engine), Philosopher (peptide and protein validation, reports), qunatitation tools, spectral library building and more.
Website GitHub
FragPipe: Proteomics 0-60 in 5 seconds
IMTBX+Grppr: Ion Mobility Toolbox + Isotopic Grouping
A suite of tools for extracting signals from Ion Mobility (IM) data (IM-MS, LC-IM-MS) and performing isotopic envelopes detection.
Website GitHub Manuscript
IMTBX+Grppr: Ion Mobility Toolbox + Isotopic Grouping