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ThermoRawFileParser
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support MonoDeepLC
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.peptide-shaker
Interpretation of proteomics identification resultsms2rescore
Modular and user-friendly platform for AI-assisted rescoring of peptide identificationssearchgui
Highly adaptable common interface for proteomics search and de novo enginesms2pip
MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.moFF
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw filecompomics-utilities
Open source Java library for computational proteomicsmeta-proteome-analyzer
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.psm_utils
Common utilities for parsing and handling peptide-spectrum matches and search engine results in PythonThermoRawFileParserGUI
Graphical user interface for the ThermoRawFileParserdenovogui
Graphical user interface for de novo sequencing of tandem mass spectraspectrum_similarity
Scoring functions to compare MS/MS spectrajsparklines
Sparklines for java tablesCOSS
COSS: CompOmics Spectral Searchingworkshop-ml-proteomics
Workshop: Tackling peptide identification ambiguity with machine learningCALLC
cellmissy
Cell Migration Invasion Storage System.lesSDRF
pout2prot
Pout2Prot converts Percolator output files to protein group and subgroup files using Occam's razor or anti-Occam's razor. These output files can directly be used in Prophane for further downstream taxonomic and functional analysispladipus
Platform for Distributed Proteomics Softwarecolims
A lims system to automate and expedite proteomics data management, processing and analysis.reporter
Protein quantification based on reporter ionsIM2Deep
Collisional cross-section prediction for modified peptidesfragmentation-analyzer
A standalone java tool for analyzing ms/ms fragmentation data.thermo-msf-parser
Parser and viewer for thermo msf files.mascotdatfile
Java API for MS/MS search results by Mascot (Matrix Science).icelogo
Next-generation visualization of protein consensus sequences by iceLogo.xilmass
An algorithm to identify cross-linked peptidesms-lims
Mass spectrometry based proteomics information management system.mumble
Finding the perfect modification for your mass shiftms2rescore-rs
Rust functionality for the MS²Rescore packagemoff-gui
A graphical user interface for the Modest Feature Finding algorithm (moFF)CellMojo
mitraq
Multiple iTRAQ/TMT Data Analysisxtandem-parser
Java-based parser for X!Tandem output xml filespride-asa-pipeline
Uniform annotation of identified spectra.tabloidProteome
elude-jwrapper
A Java API to make use of the retention time prediction functionality from elude.CompPyTools
Small Python scripts developed in the CompOmics groupReSpinOnline
Online public viewer for ReSpin Resultsspectrawl
A rich client tool used for browsing through spectra looking for specific mass differences.dbtoolkit
Manipulating fasta sequence databasesQuantPridePep
Pipeline to bring peptdie quantification in Pride using moFFsearch-all-assess-subset
An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.Tissue_prediction_manuscript
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