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 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

ms2rescore

Sensitive PSM rescoring with predicted MS² peak intensities using MS²PIP, DeepLC, and Percolator.

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