Proteome Informatics Group > Java Proteomic Library



This module provides reusable components used in the JPL:

  • - Interfaces and objects for the JPL command-line applications.
  • org.expasy.jpl.commons.base - Basic general domain component (builder, condition, io, math, ...).
  • org.expasy.jpl.commons.collection - Basic collection objects and interfaces.
  • org.expasy.jpl.commons.collection.graph - Graph objects and algorithms (extended from Jung graph library).
  • org.expasy.jpl.commons.collection.render - Statistical series and histogram renderers (jfreechart needed).

Supplied by the org.expasy.jpl.commons package.

Chemical Data

  • Contains models for simple chemical objects like atoms, molecules or amino-acids and more complex one like biological polymers.
  • Support modifiable and ionizable molecular groups.
  • Provides objects to handle molecules and polymers - mass calculator, modification handler, polymer cutter, peptide fragmenter, isoelectric point calculator, ...

Supplied by the org.expasy.jpl.core.mol package.

MS data

  • Provides Mass Spectrometry objects where a mass spectrum is presented as a peak list. In its simplest form, it contains a list of mass-to-charge values, and optionally an intensity for experimental data and/or annotation(s).
  • Provides objects that manipulate spectra like filters, intensity transformers exporters, mergers...

Supplied by the package.

MS Comparison and Alignment

Provides matchers and scorers for comparison between MS spectra.

Supplied by the msmatch package.


Provides readers/writers to import/export biological data and MS data from standards (fasta, mgf, dta, mzxml, mzml, sptxt and msp).

Supplied by the io package.


Provides models for Peptide Spectrum Match (PSM) and Peptide identifications.

Supplied by the msident package.

Cross-Platform Solution

  • Available as Open Source software under the BSD License which lets you use JPL in both commercial and Open Source programs
  • 100%-pure Java

Next Features

Here are links to the next (in-development) features for jpl packages: