CompOmics documentation

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).

Projects

ThermoRawFileParser

Thermo RAW file parser that runs on Linux with mono

ThermoRawFileParserGUI

Graphical user interface for the ThermoRawFileParser

colims

A lims system to automate and expedite proteomics data management, processing and analysis.

compomics-utilities

Open source Java library for computational proteomics

dbtoolkit

Manipulating fasta sequence databases

denovogui

Graphical user interface for de novo sequencing of tandem mass spectra

fragmentation-analyzer

A standalone java tool for analyzing ms/ms fragmentation data.

iceLogo

Next-generation visualization of protein consensus sequences by iceLogo.

jsparklines

Sparklines for java tables

jtraml

Java implementation of the PSI-MS Transitions Markup Language (TraML) specification.

mappi-dat

analysis and data management tool for high-throughput protein-protein interaction data generated from microarray-MAPPIT system

mascotdatfile

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

meta-proteome-analyzer

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

moff

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file

ms-lims

Mass spectrometry based proteomics information management system.

ms2pip_c

MS2PIP: MS2 Peak Intensity Prediction

omssa-parser

Java based parser for OMSSA OMX files

pepshell

Visualization of conformational proteomics data.

peptide-shaker

Interpretation of proteomics identification results

pladipus

Platform for Distributed Proteomics Software

pride-asa-pipeline

Uniform annotation of identified spectra.

reporter

Protein quantification based on reporter ions

search-all-assess-subset

An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.

searchgui

Highly adaptable common interface for proteomics search and de novo engines

spectrum_similarity

Scoring functions to compare MS/MS spectra

thermo-msf-parser

Parser and viewer for thermo msf files.

xilmass

An algorithm to identify cross-linked peptides

xtandem-parser

Java based parser for X!Tandem output xml files