pridepy
pridepy: A Python package to download and search data from PRIDE database - Published in JOSS (2025)
HistoJS
HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images - Published in JOSS (2024)
ionmob
An open-source prediction framework for peptide ion collision cross section (CCS) values with python.
cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
NormalyzerDE
Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.
https://github.com/bigbio/sdrf-pipelines
`sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files
mzcore
A Rust library for peptide centric mass spec calculations centered around ProForma and complex theoretical fragmentation
proteomics-sample-metadata
The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
pixelgen-pixelator
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.
https://github.com/compomics/compomics-utilities
Open source Java library for computational proteomics
PTXQC
A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
deeplc
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
alphapept
A modular, python-based framework for mass spectrometry. Powered by nbdev.
pyprophet
PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
ProtGenerics
S4 generic functions for Bioconductor mass spectrometry infrastructure
alphastats
Python Package for the downstream analysis of mass-spectrometry-based proteomics data
https://github.com/compomics/ms2rescore
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
piqmie
Proteomics Identifications & Quantitations Data Management & Integration Service
annotator
A simple tool to help you manually discover the depths of your (complex) spectra, one spectrum at a time.
mspms
R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data
proteomics-novice-qfeatures
Introduction to QFeatures, Bioconductor data object for proteomics
https://github.com/cran-task-views/omics
CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics
https://github.com/becavin-lab/bacnet
BACNET is a Java based platform to develop website for multi-omics analysis
topdownr
R-package for the analysis of Thermo Orbitrap Fusion Top-Down Proteomic Data.
https://github.com/bigbio/py-pgatk
Python tools for proteogenomics analysis toolkit
https://github.com/compomics/peptide-shaker
Interpretation of proteomics identification results
https://github.com/compomics/meta-proteome-analyzer
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
https://github.com/a-r-j/tb-resources
List of online databases and resources for Mycobacterium Tuberculosis
https://github.com/bzhanglab/pepquery
PepQuery: a targeted peptide search engine
https://github.com/compomics/mascotdatfile
Java API for MS/MS search results by Mascot (Matrix Science).
https://github.com/compomics/moff
A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
https://github.com/compomics/fragmentation-analyzer
A standalone java tool for analyzing ms/ms fragmentation data.
https://github.com/bigbio/sdrf-cellline-metadata-db
SDRF Cell Line Metadata Database
orthology_map
orthology_map is a pipeline designed to integrate suite of orthology assignment tools to contribute in a consensus based scoring algorithm
https://github.com/bigbio/pgt-pangenome
Protegenomics analysis based on Pangenome references
proteomics-data-analysis-tutorial
A comprehensive tutorial for proteomics data analysis in R that utilizes packages developed by researchers at PNNL and from Bioconductor.
https://github.com/bmascat/lfq-proteomics-pipeline
All code, bash scrypts and pipelines used to analyse and visualise proteomic data from my experiments with my first Crispr KO model.
https://github.com/bigbio/msgfplus
MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
ms2pip
MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://github.com/compomics/psm_utils
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://github.com/compomics/thermo-msf-parser
Parser and viewer for thermo msf files.
https://github.com/compomics/omssa-parser
Java based parser for OMSSA OMX files
https://github.com/compomics/im2deep
Collisional cross-section prediction for modified and multiconformational peptides
https://github.com/compomics/denovogui
Graphical user interface for de novo sequencing of tandem mass spectra
substrateminer: A Python package to investigate protein substrate repertoires
substrateminer: A Python package to investigate protein substrate repertoires - Published in JOSS (2025)
https://github.com/bigbio/pgatk-io
High performance io library for proteogenomics
https://github.com/bzhanglab/autort
AutoRT: Peptide retention time prediction using deep learning
https://github.com/compomics/xtandem-parser
Java-based parser for X!Tandem output xml files
https://github.com/compomics/spectrum_similarity
Scoring functions to compare MS/MS spectra
https://github.com/compomics/searchgui
Highly adaptable common interface for proteomics search and de novo engines
candidatevectorsearch
Searching for peptide candidates using sparse matrix + matrix/vector multiplication.
msamanda
MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.
https://github.com/bmascat/rna-seq-proteomics-pipeline
Multi-omics analysis of LFQ proteomics and transcriptomics of an ALMS1 gene knockout cell model after TGF-B pathway stimulation.
https://github.com/broadinstitute/protigy
Proteomics Toolset for Integrative Data Analysis
https://github.com/cmkobel/mspipeline1
🪆🦖 A snakemake wrapper around Nesvilab's FragPipe-CLI. In a perfect world, this pipeline was based on Sage.
metaboverse
Visualization and analysis platform for metabolic data and network pattern recognition
https://github.com/fgcz/specl
prepare peptide spectrum matches for use in targeted proteomics using R and Bioconductor
nf-encyclopedia
A NextFlow pipeline for chromatogram library DIA proteomics workflows
ptmvision
Web application for the interactive visualization and exploration of post-translational modifications of proteins from open and closed search software.
dashboard
MOMSI Standard Landscape Review Curation Workflow & Multi-Omics Dashboard
proteogendb
ProteoGenDB: A Fast Proteogenomic Pipeline for Identifying Sequence Variants in Proteomics Data
msannika
MS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra.
spatialproteomics
Cell segmentation and downstream analysis pipeline for spatial proteomics (MIBI & COMET).
https://github.com/bzhanglab/deeprescore
DeepRescore: rescore PSMs leveraging deep learning-derived peptide features
https://github.com/czbiohub-sf/protdata
Dataloader for common proteomics search engine outputs into AnnData format
https://github.com/compomics/xilmass
An algorithm to identify cross-linked peptides
quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
dynatmt
Browser-tool to analyze combined SILAC/TMT data, such as mePROD or Hyperplexing
plf
Peptide location fingerprinting (PLF) is a technique capable of identifying modified proteins and potential causal mechanisms in complex biological samples. Protein Locational Fingerprinter determines statisticaly significant peptide yields from protein functional domains.
msannika_csm_annotation
Calculates Intensities of Cross-linked Peptides from MS Annika CSMs.
https://github.com/bigbio/quantms-utils
A python library with scripts and helpers classes for quantms workflow