Proteobench / ProteoBenchView external linksLinks
ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. https://proteobench.cubimed.rub.de/
☆50Updated this week
Alternatives and similar repositories for ProteoBench
Users that are interested in ProteoBench are comparing it to the libraries listed below
Sorting:
- EuBIC-MS Developers Meeting 2025 on Computational Mass Spectrometry☆11Nov 8, 2024Updated last year
- ☆27May 20, 2025Updated 8 months ago
- Democratizing ML in proteomics☆52Feb 2, 2026Updated last week
- A Rust library for peptide centric mass spec calculations centered around PSI standards and handling complex cases robustly☆40Updated this week
- A diaPASEF spectrum-centric analysis tool☆13Dec 24, 2025Updated last month
- Proteomics search & quantification so fast that it feels like magic☆270Jan 6, 2026Updated last month
- Community-curated tutorials and datasets for ML in proteomics☆57Oct 31, 2025Updated 3 months ago
- An tandem mass spectrometry (MS/MS) sequence database search tool.☆53Feb 3, 2026Updated last week
- Fast and flexible semi-supervised learning for peptide detection in Python☆49Feb 27, 2025Updated 11 months ago
- Fast and accurate label-free quantification for small and very large numbers of proteomes☆60Jan 7, 2026Updated last month
- A Python interface to proteomics data repositories☆36Jun 19, 2025Updated 7 months ago
- Infrastructure of AlphaX ecosystem☆53Jan 30, 2026Updated 2 weeks ago
- A python interface to the SAGE search engine for mass spectrometry proteomics☆15Jan 16, 2026Updated 3 weeks ago
- High quality in silico spectral library generation for data-independent acquisition proteomics☆16Nov 6, 2025Updated 3 months ago
- Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python☆29Dec 22, 2025Updated last month
- Library for mass spectrometry projects☆27Updated this week
- CLI toolkit for fast analysis of DIA proteomics experiments and in silico library prediction☆19Updated this week
- EuBIC 2023 developer's meeting☆13Jan 16, 2023Updated 3 years ago
- A deep learning toolkit for mass spectrometry☆87Jan 7, 2026Updated last month
- Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities☆107Feb 6, 2026Updated last week
- ☆38Feb 5, 2026Updated last week
- Python framework for Deep Learning in Proteomics☆38Updated this week
- Rescoring and spectral library generation pipeline for proteomics.☆53Feb 4, 2026Updated last week
- Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provi…☆150Feb 5, 2026Updated last week
- Python client for PRIDE Archive Rest API.☆36Feb 6, 2026Updated last week
- Imputing proteomics data using deep learning models☆31Nov 12, 2025Updated 3 months ago
- Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments☆13May 23, 2025Updated 8 months ago
- HUPO-PSI Standardized peptidoform notation☆23Nov 14, 2025Updated 2 months ago
- ☆31Dec 7, 2025Updated 2 months ago
- Modular and user-friendly platform for AI-assisted rescoring of peptide identifications☆62Jan 28, 2026Updated 2 weeks ago
- ☆21Feb 14, 2025Updated 11 months ago
- Prediction of glycopeptide fragment mass spectra by deep learning☆10Feb 20, 2024Updated last year
- ☆19Feb 5, 2026Updated last week
- This repository attempts to implement a neural net that leverages the transformer architecture to predict peptide properties (retention t…☆11Nov 22, 2024Updated last year
- Data Processing Kitchen Sink for proteomics data☆13Jan 13, 2026Updated last month
- Repository for Deep Learning Models for Mass Spectrometry written in Rust☆16Dec 30, 2025Updated last month
- A Framework for IMS-MS Raw Data Processing written in Rust and Python.☆19Feb 6, 2026Updated last week
- MaxQuant and Perseus Bug Reporting☆11Mar 19, 2025Updated 10 months ago
- Semi-supervised learning for peptide identification from shotgun proteomics datasets☆142Nov 21, 2025Updated 2 months ago