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.

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](http://search.maven.org/#search%7Cga%7C1%7Ca%3A%22msftbx%22).

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.

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.