Repositories list

• FragPipe

  Public
  A cross-platform proteomics data analysis suite

  guiproteomicsmass-spectrometry+ 5

  guiproteomicsmass-spectrometrylabel-free-quantificationcommand-line-interfaceisobaric-quantificationdata-independent-acquisitiondata-dependent-acquisition

  Java

  •

  Other

  •4747 forks•315315 stars•4141 issues•11 pull request•Updated Aug 2, 2026Aug 2, 2026

• FragSummarizer

  Public
  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• philosopher

  Public
  PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

  gobioinformaticsdata-analysis+ 3

  gobioinformaticsdata-analysisproteomicsmass-spectrometryms-data

  Go

  •

  GNU General Public License v3.0

  •2222 forks•128128 stars•5353 issues•00 pull requests•Updated Jul 18, 2026Jul 18, 2026

• MSBooster

  Public
  MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

  Java

  •

  GNU Lesser General Public License v3.0

  •22 forks•2222 stars•00 issues•00 pull requests•Updated Jul 18, 2026Jul 18, 2026

• FragPipeAnalystR

  Public
  R

  •

  GNU General Public License v3.0

  •44 forks•99 stars•1111 issues•55 pull requests•Updated Jul 16, 2026Jul 16, 2026

• nesvilab.github.io

  Public
  Nesvilab website

  Less

  •

  Apache License 2.0

  •22 forks•11 star•00 issues•00 pull requests•Updated Jul 15, 2026Jul 15, 2026

• PepCentric

  Public
  Search proteins and peptides against repository-scale MS/MS spectra within seconds

  proteomicsproteogenomics

  proteomicsproteogenomics

  00 forks•11 star•00 issues•00 pull requests•Updated Jun 25, 2026Jun 25, 2026

• TMT-Integrator

  Public
  A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.

  Java

  •

  Apache License 2.0

  •22 forks•1414 stars•11 issue•00 pull requests•Updated Jun 25, 2026Jun 25, 2026

• pwiz

  Public
  The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.

  C#

  •

  Apache License 2.0

  •119119 forks•00 stars•00 issues•00 pull requests•Updated Jun 17, 2026Jun 17, 2026

• FragPipe-SpecLib

  Public
  FragPipe-SpecLib: Simple library generation for FragPipe

  proteomicsdata-independent-acquisitionspectral-library+ 1

  proteomicsdata-independent-acquisitionspectral-libraryfragpipe

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork•00 stars•11 issue•11 pull request•Updated May 29, 2026May 29, 2026

• FragPipe-PDV

  Public
  A forked PDV for FragPipe

  Java

  •

  GNU General Public License v3.0

  •2222 forks•11 star•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• FragPipe-Analyst

  Public
  Documentation is available here:

  HTML

  •

  GNU General Public License v3.0

  •1414 forks•00 stars•00 issues•88 pull requests•Updated May 19, 2026May 19, 2026

• MSFragger-RTS-client

  Public
  MSFragger real-time searching C# client

  C#

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 8, 2026May 8, 2026

• PTM-Shepherd

  Public
  A tool for summarizing open search results

  Java

  •

  Apache License 2.0

  •88 forks•1616 stars•00 issues•00 pull requests•Updated May 5, 2026May 5, 2026

• FragAnnotator

  Public
  Add matched fragments to psm.tsv

  Java

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• diaTracer

  Public
  A diaPASEF spectrum-centric analysis tool

  proteomicsdiadiapasef

  proteomicsdiadiapasef

  22 forks•1414 stars•33 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• MSFragger

  Public
  Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

  bioinformaticsproteomicsmass-spectrometry+ 1

  bioinformaticsproteomicsmass-spectrometrydatabase-search

  HTML

  •1212 forks•132132 stars•11 issue•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• PepCentric-manuscript

  Public
  Scripts to generate the results in the PepCentric paper

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 15, 2026Mar 15, 2026

• FragPipe-Analyst-doc

  Public
  An easy-to-use and interactive web application for FragPipe

  33 forks•1515 stars•77 issues•00 pull requests•Updated Mar 8, 2026Mar 8, 2026

• MBG

  Public
  match between glycans

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 4, 2026Mar 4, 2026

• clean-storage

  Public
  A shell script to clean the Storage. Internal use only. DISCLAIMER: not responsible for loss of data.

  Shell

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 26, 2026Feb 26, 2026

• DIA-Umpire

  Public
  Computational analysis for mass spectrometry-based proteomics data

  Java

  •

  GNU General Public License v3.0

  •1010 forks•2121 stars•22 issues•00 pull requests•Updated Feb 22, 2026Feb 22, 2026

• list-PRIDE

  Public
  Query and list all projects from PRIDE

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• msconvert-scripts

  Public
  Some shell scripts related to Thermo Fisher raw format conversion using msconvert

  Shell

  •

  Apache License 2.0

  •33 forks•1515 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• Crystal-C

  Public
  Crystal-C: A computational tool for refinement of open search results

  Java

  •

  Apache License 2.0

  •44 forks•66 stars•22 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• EntrapBench

  Public
  Generate entrapment database and calculate false discovery proportion (FDP)

  Java

  •

  Apache License 2.0

  •11 fork•55 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• SpecLibIO

  Public
  A Java library for reading and writing DIA-NN spectral library files (`.speclib` format).

  Java

  •

  Apache License 2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• TMT-Integrator-manuscript

  Public
  R

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 9, 2026Feb 9, 2026

• MSFragger-DDAPlus-Manuscript

  Public
  Python and R scripts to generate the figures in the MSFragger-DDA+ paper

  Jupyter Notebook

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 9, 2026Feb 9, 2026

• diaTracer-manuscript

  Public
  R

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 9, 2026Feb 9, 2026