RawConverter on proteomicsyates by the lab of John R. Yates III

PINT is a new comprehensive web-based system to store, visualize, and query experimental proteomics data obtained under different experimental conditions and projects. PINT provides a very powerful query system through the use of different proteomics-specific data query commands running over both the experimental features and external annotation…

General Java util classes used across different projects

Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).

extension of dbIndex module to index proteoforms

Parser for quantitative data from files created by Census software.

Indexing of FASTA files for searching peptide masses and sequences

Based on Jmol, it calculates the surface accessibility of specific sites in a given protein. Optionally it measures the distances between specific atoms of specific sites in the structure of the protein

Fast and flexible semi-supervised learning for peptide detection in Python

This is a Java stand-alone tool for the quantitation of glyco sites. It calculates the proportion of different glyco-PTMs in a protein of interest. It supports data from IP2 (quant compare output files) and MaxQuant.