Welcome to the website for software projects created and maintained by the Computational Omics and Systems Biology Group (Compomics). Below you can find a list of software we have developed, and on the subsequent pages are documentation and links to downloads and source code (hosted on Github).
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
Graphical user interface for the ThermoRawFileParser
A lims system to automate and expedite proteomics data management, processing and analysis.
Open source Java library for computational proteomics
Manipulating fasta sequence databases
Graphical user interface for de novo sequencing of tandem mass spectra
A standalone java tool for analyzing ms/ms fragmentation data.
Next-generation visualization of protein consensus sequences by iceLogo.
Sparklines for java tables
Java implementation of the PSI-MS Transitions Markup Language (TraML) specification.
analysis and data management tool for high-throughput protein-protein interaction data generated from microarray-MAPPIT system
Java API for MS/MS search results by Mascot (Matrix Science).
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Mass spectrometry based proteomics information management system.
MS2PIP: MS2 Peak Intensity Prediction
Sensitive PSM rescoring with predicted MS² peak intensities using MS²PIP, DeepLC, and Percolator.
Java based parser for OMSSA OMX files
Visualization of conformational proteomics data.
Interpretation of proteomics identification results
Platform for Distributed Proteomics Software
Uniform annotation of identified spectra.
Protein quantification based on reporter ions
An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.
Highly adaptable common interface for proteomics search and de novo engines
Scoring functions to compare MS/MS spectra
Parser and viewer for thermo msf files.
An algorithm to identify cross-linked peptides
Java-based parser for X!Tandem output xml files