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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 proteomicspsm_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 learningscop3d
Sequence conservation of protein on 3D structure.CALLC
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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