Download JAR files tagged by mass with all dependencies

PeakInvestigator™ is advanced centroiding and deconvolution software services for mass spectrometry. This library provides an object-oriented interface to its public API.

Library for general purpose in silico chemistry, mainly intended for mass spectrometry proteomics computations.

Library allowing generation of plots and data from proteomics and metabolomics mass spectrometry data through the use of R and java methods.

Protein inference toolbox that contains algorithms to merge results from search engines in mass spectrometry and proteomics. It provides functionalities to compute FDR at different levels including PSM, peptide and Protein levels.

The jmzReader library is a collection of parsers to process the most commonly used Mass Spectrometry text and xml based file formats using a single interface.

X-Tracker is a PSI-standards-compliant software framework for supporting mass spectrometry-based protein quantitation. Through an abstraction of the main steps involved in quantitation, X-Tracker should technically be able to support quantitation by means of all the current protocols, both at MS1 and/or MS2 level, and provide a flexible, platform-independent quantitation environment.

Maltcms, short for "Modular Application Toolkit for Chromatography Mass-Spectrometry" is an application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. Its aim is to provide reusable, efficient datastructures, abstracting from the various low-level data-formats like netcdf (ANDIMS), mzXML, mzData and mzML and providing consistent access to data features like mass spectra, chromatograms and metadata. Furthermore, Maltcms provides a platform for the implementation and execution of processing pipelines. New and existing algorithms can be easily implemented or included and executed together with existing processing elements.