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
deeplc

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

The server edition of the iceLogo tool.
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.
ms-lims

Mass spectrometry based proteomics information management system.
ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
ms2rescore

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

Java front end to the ontology lookup service (OLS)
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
tabloidproteome

None
thermo-msf-parser

Parser and viewer for thermo msf files.
xtandem-parser

Java-based parser for X!Tandem output xml files