library

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
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