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

DeepLC

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
ThermoRawFileParser

Thermo RAW file parser that runs on Linux/Mac and all other platforms that support 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
ms2rescore

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
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