Data and text mining JAMSS: proteomics mass spectrometry simulation in Java

Summary: Countless proteomics data processing algorithms have been proposed, yet few have been critically evaluated due to lack of labeled data (data with known identities and quantities). Although labeling techniques exist, they are limited in terms of confidence and accuracy. In silico simulators have recently been used to create complex data with known identities and quantities. We propose Java Mass Spectrometry Simulator (JAMSS): a fast, self-contained in silico simulator capable of generating simulated MS and LC-MS runs while providing meta information on the provenance of each generated signal. JAMSS improves upon previous in silico simulators in terms of its ease to install, minimal parameters, graphical user interface, multithreading capability, retention time shift model and reproducibility. Availability and implementation: The simulator creates mzML 1.1.0. It is open source software licensed under the GPLv3. The software and source are available at https://github.com/optimus moose/JAMSS. Contact: [email protected]