mass-spectrometry

BatMass

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).

IMTBX+Grppr

A suite of tools for extracting signals from Ion Mobility (IM) data (IM-MS, LC-IM-MS) and performing isotopic envelopes detection.

MSFragger

Ultra-fast proteomics search engine. Regular searches - when the precursor mass is limited to a narrow window of several ppm - are done within a few seconds. An "open-search" (with large precursor mass range tolerance, e.g. +/-500 Da) for a 2 hour LC gradient bottom-up proteomics experiment can be done in a minute or so on a laptop.

DIA-Umpire

Data Independent Acquisition (DIA) data processing tool that doens't require a spectral library. Detects features in MS1 and MS2, correlates precursors to fragments based on elution profile and compiles pseudo-MS/MS spectra which can be searched with standard proteomic search tools.