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Allows users to process mzML files using Java programming language. jmzML is a mature Java application programming interface (API) for mzML files that combines a small memory footprint with a fully functional object model, including automatic XML reference resolving without sacrificing the overall speed of data access. This software comes with an interactive mzML viewer that can be used to load and view spectra and chromatograms from multiple, very large mzML files simultaneously.


A mass spectrometry data converter. RawConverter provides the ability to take advantage of the high resolution and accuracy provided by the latest Thermo Fisher instruments. RawConverter extracts mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data from RAW files like its predecessor RawXtract but also selects the correct precursor mass-to-charge (m/z) ratios. It accepts RAW data generated by either data-dependent acquisition (DDA) or data-independent acquisition (DIA). The output file format can be MS1/MS2, MGF or mzXML.


Allows to read, write and validate mzTab files. jmzTab is an open source Java application programming interface for to supporting the Proteomics Standards Initiative (PSI)’s mzTab standard format. The software simplifies accessing the information included in mzTab files, thereby promoting its use and facilitating its support in third party software. jmzTab is structured in a three-layer architecture: (i) the Core Model Layer, (ii) the Enhancement Utilities Layer and (iii) the Standalone Application Layer.

Thermo Raw File Reader

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Provides several methods for parsing the information returned by MSFileReader. Thermo Raw File Reader is a package that demonstrates how to read Thermo-Finnigan .Raw files using Thermo's MS File Reader. It offers some functions to determine the parent ion m/z and fragmentation mode in a given scan filter, to determine the ionization mode from a given scan filter, to extract multiple reaction monitoring (MRM) masses listed in a given scan filter and many others.