Alternatives and similar repositories for Informed-Proteomics

Users that are interested in Informed-Proteomics are comparing it to the libraries listed below

• PNNL-Comp-Mass-Spec / DeconTools

  View on GitHub
  Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
  ☆19Oct 23, 2025Updated 3 months ago
• smith-chem-wisc / mzLib

  View on GitHub
  Library for mass spectrometry projects
  ☆27Updated this week
• nwamsley1 / Pioneer.jl

  View on GitHub
  CLI toolkit for fast analysis of DIA proteomics experiments and in silico library prediction
  ☆19Feb 7, 2026Updated last week
• MSGFPlus / msgfplus

  View on GitHub
  MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence …
  ☆83Oct 23, 2025Updated 3 months ago
• dbaileychess / CSMSL

  View on GitHub
  C# Mass Spectrometry Library
  ☆38Jun 14, 2022Updated 3 years ago
• Villen-Lab / pyAscore

  View on GitHub
  A python package for fast post translational modification localization, powered by Cython.
  ☆20Dec 15, 2023Updated 2 years ago
• mhoopmann / kojak

  View on GitHub
  Automatically exported from code.google.com/p/kojak-ms
  ☆13Apr 11, 2025Updated 10 months ago
• smith-chem-wisc / FlashLFQ

  View on GitHub
  Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
  ☆23Jul 25, 2025Updated 6 months ago
• statisticalbiotechnology / triqler

  View on GitHub
  The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code
  ☆26Oct 2, 2025Updated 4 months ago
• frallain / pymsfilereader

  View on GitHub
  Thermo MSFileReader Python bindings
  ☆69May 4, 2021Updated 4 years ago
• fickludd / dinosaur

  View on GitHub
  Feature finding algorithm for detection of isotope patterns in HPLC mass spectrometry data.
  ☆45Jun 27, 2022Updated 3 years ago
• michaelmarty / UniDec

  View on GitHub
  Universal Deconvolution of Mass and Ion Mobility Spectra
  ☆83Feb 6, 2026Updated last week
• thermofisherlsms / iapi

  View on GitHub
  Instrument Application Programming Interface
  ☆51Sep 29, 2025Updated 4 months ago
• UWPR / Lorikeet

  View on GitHub
  Lorikeet is a JQuery plugin to view MS/MS spectra annotated with fragment ions.
  ☆17Sep 7, 2023Updated 2 years ago
• medbioinf / pia

  View on GitHub
  PIA - Protein Inference Algorithms
  ☆24Jan 22, 2026Updated 3 weeks ago
• HUPO-PSI / psi-ms-CV

  View on GitHub
  HUPO-PSI mass spectrometry CV
  ☆40Jan 30, 2026Updated 2 weeks ago
• CompOmics / moFF

  View on GitHub
  A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
  ☆33Apr 19, 2021Updated 4 years ago
• MatteoLacki / IsoSpec

  View on GitHub
  Libraries for fine isotopic structure calculator.
  ☆41Feb 3, 2026Updated last week
• kevinkovalchik / RawTools

  View on GitHub
  RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control ana…
  ☆67Jan 6, 2026Updated last month
• kusterlab / picked_group_fdr

  View on GitHub
  Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
  ☆13May 23, 2025Updated 8 months ago
• PNNL-Comp-Mass-Spec / LIQUID

  View on GitHub
  Software tool for identifying lipids in LC-MS/MS-based lipidomics data
  ☆22Apr 13, 2022Updated 3 years ago
• pFindStudio / pDeep3

  View on GitHub
  MS/MS prediction for peptides
  ☆24Dec 18, 2020Updated 5 years ago
• pFindStudio / pDeepXL

  View on GitHub
  pDeepXL: MS/MS spectrum prediction for cross-linked peptide pairs by deep learning
  ☆12Feb 8, 2021Updated 5 years ago
• smith-chem-wisc / MetaMorpheus

  View on GitHub
  Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
  ☆107Feb 6, 2026Updated last week
• singjc / redeem

  View on GitHub
  Repository for Deep Learning Models for Mass Spectrometry written in Rust
  ☆16Dec 30, 2025Updated last month
• theGreatHerrLebert / rustims

  View on GitHub
  A Framework for IMS-MS Raw Data Processing written in Rust and Python.
  ☆19Feb 6, 2026Updated last week
• HUPO-PSI / mzIdentML

  View on GitHub
  Repository for mzIdentML and the corresponding examples
  ☆26Jan 16, 2026Updated 3 weeks ago
• PRIDE-Archive / pridepy

  View on GitHub
  Python client for PRIDE Archive Rest API.
  ☆36Feb 6, 2026Updated last week
• smith-chem-wisc / MetaNetwork

  View on GitHub
  ☆12Jan 14, 2023Updated 3 years ago
• cpanse / protViz

  View on GitHub
  Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
  ☆11Jun 3, 2025Updated 8 months ago
• CompOmics / ms2pip

  View on GitHub
  MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
  ☆48Updated this week
• mhoopmann / mstoolkit

  View on GitHub
  Automatically exported from code.google.com/p/mstoolkit
  ☆30Dec 1, 2025Updated 2 months ago
• UWPR / Comet

  View on GitHub
  An tandem mass spectrometry (MS/MS) sequence database search tool.
  ☆53Feb 3, 2026Updated last week
• bittremieuxlab / ANN-SoLo

  View on GitHub
  Spectral library searching using approximate nearest neighbor techniques.
  ☆48Updated this week
• MannLabs / timsrust

  View on GitHub
  ☆27May 20, 2025Updated 8 months ago
• MannLabs / alphapept

  View on GitHub
  A modular, python-based framework for mass spectrometry. Powered by nbdev.
  ☆185Apr 19, 2024Updated last year
• MannLabs / alphapeptdeep

  View on GitHub
  Deep learning framework for proteomics
  ☆145Jan 30, 2026Updated 2 weeks ago
• msproteomicstools / msproteomicstools

  View on GitHub
  Some hopefully useful tools for mass spectrometry applied to proteomics
  ☆53Oct 12, 2021Updated 4 years ago
• ms-numpress / ms-numpress

  View on GitHub
  Implementations of compression schemes for numeric data from mass spectrometers.
  ☆13Mar 3, 2021Updated 4 years ago