Open source java library for computational proteomics

JAXB implementation of the mzML 1.1 standard as made available from the Proteomics Standards Initiative. This object model can be used to serialize/deserialize properly formed mzML XML files.

Interpretation of proteomics identification results

Protein quantification based on reporter ions

Graphical user interface for proteomics identification search engines

An exhaustive database of theoretically generated lipids manually curated with experimental evidence

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.

Java based parser for OMSSA (Open Mass Spectrometry Search Algorithm) omx files

Graphical user interface for de novo sequencing of tandem mass spectra

Dbtoolkit

Java API for MS/MS search results by Mascot (Matrix Science)