Presented are a number of links to proteomic and protein databases as well as tools for Mass Spectrometry and Data Visualisation. These are currently mainly generic or associated with human biology and diseases but there are sections that include other organisms. Please let Pastel BioScience know ( of other databases that may be useful to the proteomics community.

We haven't referenced the original publications for these but with a little detective work I'm sure they can be easily found, and if not, please reach out to the X (ex Twitter) and/or Mastodon communities for help :-)

This page is currently being updated (230725) as many of the sites/links are no longer working. Old sites/links that no longer work are archived at the bottom of the page as a historical reference. Some sites, whose link still work but are considered very old (pre 2013, arbitrarily over 10 years old), are also archived at the bottom of the page.

Given the number of entries this may take quite some time, please be patient :-)

Main Proteomics Databases Currently in Use


.....Includes Blast, Align, Peptide Search, ID Mapping and Sparkle

ExPaSy | Swissprot

.....Includes a huge resource of programs, scripts and sub-databases - well worth a re-visit avery now and then to remind oneself of how much there is :-)


.....EBI resources and Tools of which there are 159 !!! Including things like AlphaFold-DB, OMICS-DI, Complex Portal, InterPro

NCBI - The Protein Database

NCI - Proteomic Data Commons




Panorama - repository from Skyline


neXtProt | exploring the universe of human proteins

…..neXtProt - tools | peptide uniqueness checker


iProX | integrated proteome resources center in China

wwPDB | open access to high-quality 3D structural biology data

PIR | Protein Information Resource

Human Protein Atlas

Human Proteome Map

hu.MAP | Human Protein Complex Map


…..GPMDB Proteome Database

CHESS-3 | includes link to CHESS protein DB

SubCell BarCode | web portal to proteome subcellular localization

ProteomicsDB | DB using SAP HANA from Technische Universitat Munchen

CTPD | proteoform atlas from top-down proteomics

APPRIS | annotating principal splice isoforms

Superfamily 2.0

CHPP | Chromosome-centric Human Proteome Project

Proteome Quality Index | using comprehensive database of downloadable proteomes

bioDBnet | integrates biological DBs e.g. Gene, UniProt, Ensembl, GO, Affy, RefSeq etc

EncoMPASS | Membrane Proteins Analyzed by Structure and Symmetry

SmProt | database of small proteins encoded by annotated coding & non-coding RNA loci

SAAVpedia | analysis pipeline to prioritize and interpret SAAVs

QCPA | Quantitative Cell Proteomic Atlas

DBSAV | GTS and DeepSAV scores of SAVs in human genes

The Unknome project | ranks proteins based on how little is known about them | 2023


UniProtR | retrieval in addition to screening visualization tool, & ID conversion

PPX | a python interface to proteomics data repositories

HPAanalyze | R package to retrieve & analyze data from the HPA

Recently added (2024 = 35 so far) - no particular order

Gygi Lab Softare | 2024

SumoPred-PLM | human SUMOylation & SUMO2/3 sites prediction | 2024

CombFold | predicting structures of large protein assemblies | 2024

MRMPro | improves speed of manual calibration for MRM data analysis | 2024

PMIpred | predicts protein-membrane interactions | 2024

ADAMS | GPU-Accelerated protein structre comparison | 2024

CoSpred | complete MSMS spectrum prediction workflow | 2024

StoneMod 2.0 | database & prediction of kidney stone modulatory proteins | 2024

OpenProt 2.0 | functional characterization of alternative proteins | 2024

MiCId GUI | Microorganism Class. & Ident. workflow | 2024

Foldy | interactive protein structure analysis | 2024

RawVegetable 2.0 | QC software with specialized modules for XLMS experiments | 2024

LukProt | database of eukaryotic predicted proteins for investigations of animal origins | 2024

Rapid QC-MS | Interactive Dashboard for Synchronous MS Data Acquisition QC | 2024

ALBATROSS | pRoperties Of diSordered proteinS | 2024

PgxSAVy | evaluation of variant peptide quality in proteogenomics | 2024

Aqueous Humor Proteomics Database | 2024

MS²Rescore 3.0 | boost peptide identifications | 2024

ProteomicsML | datasets for machine learning models in the field of proteomics | 2024

DIAgui | process the output from DIA-NN | 2024

Autoprot | processing, analysis & vis. of proteomics data | 2024

SpliceProt 2.0 | Sequence Repository of Human, Mouse, & Rat Proteoforms | 2024

iSanXoT: | integrative analysis of MS-based quant. proteomics data | 2024

MassDash | Targeted Mass Spectrometry Visualization | 2024

ProteinMPNN | Complex Sequence Properties of Transmembrane β-barrels | 2024

SpectraX | Principal Component Analysis-Based Spectral Analysis | 2024

SCPlainer | MS-Based Single-Cell Proteomics Data Analysis | 2024

DeepRescore2 | boost phosphoproteomics-based discoveries through improved phosphopeptide ident. | 2024

Seq-InSite | Sequence-based Interaction Site prediction | 2024

FLAMS | Find Lysine Acylations & other Modification Sites | 2024

CoVProt 2.0 | Covid Proteome Database | 2024

The Proteomes that Feed the World | 2024

Orsburn Lab Software | 2024

GlyComb | glycoconjugate data repository for glycomics & proteomics | 2024

Genomics 2 Proteins portal | linking genetic screening outputs to protein seq. & structures | 2024

Recently added (2023 = 168) - approx reverse date order

msTrawler | analyzing multiplexed proteomics data with a reliability threshold & accounting for heteroskedactity | 2023

FunPrediCATH | protein function prediction method based on CATH | 2023

iProPhos | proteome and phosphoproteome analysis | 2023

PDBImages | images of macromolecular structures from mmCIF or binary CIF structure files based on Mol* | 2023

DeepRTAlign | retention time alignment tool for large cohort LC-MS data analysis | 2023

CytoCopasi | chemical systems biology target & drug discovery visual data analytics platform | 2023

O-GlcNAcPRED-DL | prediction of protein O-GlcNAcylation Sites | 2023

MPP |predicting & visualizing physiochemical properties of proteins at proteome level | 2023

MechanoPro-DB | database of mechanical properties of proteins | 2023

CLIPPER 2.0 | peptide-level annotation software used natively in pipeline with Proteome Discoverer & Spectromine/Spectronaut | 2023

Wombat-p pipelines | analysis of label-free proteomics data | 2023

DeepProSite | identifying protein binding sites using protein structure & seq. info | 2023

DIGEST | designing of multiple reaction monitoring assays | 2023

PepCNN | uses structure & seq.-based info from primary protein seqs. to predict peptide-binding residues | 2023

Matchms | import, process, clean, and compare MS/MS data | 2023

Cardinal v3 | mass spectrometry imaging analysis | 2023

Expression Atlas | sequencing data at single cell level | 2023

Expression Atlas | sequencing data at bulk cell level | 2023

DIDAR | assessing quality of multiplexed single cell proteomics data | 2023

Yeast Protein-Protein-Interaction Network | 2023

SSDraw pub.-quality protein secondary structure diagrams from 3D protein structures | 2023

FLASHQuant | proteoform quantification in top-down proteomics | 2023

DescribePROT | DatabasE of StruCtuRe and functIon residue-Based prEdictions of PROTeins | 2023

AFRbase | Antifungal Resistance DB with amino-acid mutations affecting resistance profiles | 2023

GRable | site-specific glycan compositions of glycopeptides, using Glyco-RIDGE method | 2023

Pepid: | bioinformatics-oriented peptide search engine | 2023

CrypticProteinDB | database of proteome & immunopeptidome derived non-canonical cancer proteins | 2023

iBAQ | abundance of a protein by dividing total precursor intensities by number of theoretically observable peptides of the protein | 2023

A3D | database for proteome aggregation predictions in model organisms | 2023

PICKLUSTER | protein-interface clustering & analysis plug-in for UCSF ChimeraX | 2023

Struct2GO | protein function prediction based on graph pooling algo. & AlphaFold2 structure info. | 2023

CAAStools | identify & test Convergent Amino Acid Substitutions | 2023

KINtaro| protein kinase-like (PKL) families of Legionella pankinome | 2023

CC+ | validated coiled coils in PDB structures & AlphaFold2 models | 2023

PCDDB | a public repository for circular dichroism spectral data | 2023

MFPPDB | multi-functional plant peptide database | 2023

OmicsSuite | analysis & visualization of multi-omics big data | 2023

DIALib-QC v1.2 | analyze DIA libraries in formats of PeakView, OpenSWATH, Spectronaut & Predicted ion libraries | 2023

CancerProteome| a database to decipher proteome landscape across various cancer types | 2023

Sage | fast proteomics searching & quantification at scale | 2023

HeapMS | peak-picking pipeline for targeted proteomic data powered by 2D heatmap transformation & CNN | 2023

CUDASW++4.0 | Smith-Waterman Protein Seq. Database Search *link broken | 2023

SingPro | database of raw data, experimental detail, & protein expression profile for MS & flow-cyto single-cell proteomic studies | 2023

NMPFamsDB | database of novel protein families from microbial metagenomes & metatranscriptomes | 2023

DeepPeptide | predicts cleaved peptides in proteins using conditional random fields *link problematic| 2023

MsQuality | quality metric calculation from spectra & MS data | 2023

hplc-py | accurate & efficient peak detection & quant. from chromatography data | 2023

Chlamydomonas Library Project (CLiP) | incl. spatial proteomics data | 2023

ProteinCartography | comparing proteins with structure-based maps for interactive exploration | 2023

Nphos | database & predictor of protein N-phosphorylation | 2023

SBILib | handle for protein modeling & engineering | 2023

UK Biobank Pharma Proteomics Project (UKB-PPP) | 2023

UDock2 | multi-body protein-protein docking software | 2023

WOMBAT |WOrkflow Metrics, Benchmarking & AnalyTics | 2023

TopDownApp | analysis & vis. of top-down proteomics data | 2023

DeepGOWeb | predicting protein functions based on protein seq. | 2023

Hefeweizen yeast | proteomic profiling across fermentation | 2023

DeepUMQA | USR-based model QA method for single protein (monomer) structure & multimeric complexes | 2023

pLM-BLAST|distant homology detection from protein language models | 2023

AlphaMissense | proteome-wide missense variant effect prediction | 2023

PMIpred | predicts protein-membrane interactions for peptides & proteins | 2023

HPC-Atlas | atlas of human protein complexes | 2023

SEPepQuant | protein isoform characterization in shotgun proteomics | 2023

ZEPPI | proteome-scale seq.-based evaluation of protein-protein interfaces | 2023

AQcalc | identifies weak molecular interactions in protein structures | 2023

FLIBase | repository of full-length isoforms across human cancers & tissues | 2023

PeptideBERT | peptide propertyprediction | 2023

Oktoberfest | spectral library generation & rescoring pipeline | 2023

Pep-CNN | predicting therapeutic peptides based on convolutional neural network | 2023

MAGPIE: vis. & analyzing simultaneous protein interactions with binding partner | 2023

FunTaxIS-lite | investigates protein functions in all living organisms | 2023

InflectSSP | analysis of thermal proteome profiling | 2023

3Dmapper | maps annotated genomic variants or positions to protein structures | 2023

Ionmob |prediction of peptide collisional cross-section values | 2023

PTMNavigator | vis. of diff. reg. PTMs in cellular signaling pathways | 2023

DeepRTAlign | retention time alignment tool for large cohort LC-MS data analysis | 2023

ParSe v2 | predict phase-separating protein regions from primary seq. | 2023

SCP Viz | interface for single protein analysis in single cell proteomics datasets | 2023

ReCom | ultra-tolerant database search for identification of peptide PTMs| 2023

pyScoMotif | similar 3D structural motifs across proteins | 2023

SSDraw | generates publication-quality protein secondary structure diagrams from 3D protein structures | 2023

iSanXoT | integrative analysis of MS-Based quantitative proteomics data | 2023

HowDirty | evaluates molecular contaminants in LC-MS experiments | 2023

GlyCosmos Portal v3.3.0 | integration of glycosciences with life sciences | 2023

ProteoArk | data analysis and data visualization | 2023

DeepSCP | deep learning to boost single-cell proteome coverage | 2023

SpatialSort | spatial bayesian clustering for incorporation of prior biological knowledge | 2023

SPAT | scores proteins according to chance of location at cell surface | 2023

nf-encyclopedia | NextFlow pipeline designed to analyze DIA proteomics that leverage chromatogram libraries | 2023

SabBox | online structural antibody database & tools | 2023

pmultiqc | pipeline performance of MS based quantification pipelines | 2023

ProteStAr | compress collections of files describing protein structures PDB, mmCIF, PAE | 2023

PANDORA v2.0 | anchor restrained modelling pipeline for generating peptide-MHC structures | 2023

MS²Rescore | peptide identification rescoring with predicted spectra using MS²PIP, DeepLC & Percolator | 2023

VoltRon | spatial omic analysis toolbox for multi-omics integration using spatial image registration | 2023

FragPipe-Analyst | differential expression analysis of LFQ-MBR, TMT & DIA quantification workflows| 2023

quantms | cloud-based pipeline for proteomics reanalysis | 2023

DBLiPro | database for Lipids & proteins in human lipid metabolism | 2023

BamQuery | proteogenomic tool to explore immunopeptidome & actionable tumor antigens | 2023

BioCypher | democratising knowledge graphs (KGs) | 2023

Phospho-Analyst | interactive web platform to analyze quantitative phosphoproteomics data | 2023

IQMMA | MS1 Intensity Extraction Pipeline for DDA Proteomics | 2023

MS Annika 2.0 | cross-linking search engine for use with cleavable cross-linkers and MS2 or MS2-MS3 spectra | 2023

Matrisome AnalyzeR | identifies matrisome molecules (e.g., genes, transcripts, proteins) in -omic datasets & annotates & tabulates these molecules | 2023

MineProt | server for structural proteome curation | 2023

DeepPPAPred | deep learning-based binding affinity prediction tool for proteins | 2023

ProteoMixture | cell type deconvolution for bulk tissue proteomics data | 2023

COVIDpro | database for mining protein dysregulation in patients with COVID-19 | 2023

phuEGO | reconstruct active signalling pathways from phosphoproteomics datasets | 2023

TALAIA | a 3D visual dictionary for protein structures | 2023

CCDUtils | h&ling & analysing small molecules in thePDBe | 2023

metaSpectraST | metaproteomic MS/MS data using spectrum clustering | 2023

CoCoNat | deep-learning for coiled-coil prediction | 2023

SHEPHARD | analyzing & annotating large protein datasets | 2023

PCGAN | protein complex identification from protein interaction networks | 2023

DC-MAPP |analysis of mass spectral data to identify peptide/protein seqs. | 2023

IsoMatchMS | annotation & visualization of high Res. MALDI-MS Spectra | 2023

AlphaPeptStats | statistical analysis of MS-based proteomics | 2023

ProteomeGenerator2 | integrates genome & transcriptome seq. to incorporate protein variants | 2023

The Unknome project | ranks proteins based on how little is known about them | 2023

Cell Cycle database (CCdb) | 2023

jMorp | proteome data for plasma from >5000 healthy Japanese volunteers | 2023

The Human Skin Atlas | 2023

Breast Cancer Proteome Portal | 2023

CurtainPTM | exploration & sharing of MS-based proteomics PTM data | 2023

HowDirty | assesses the level of contamination of LC-MS results | 2023

einprot | workflows for statistical analysis of quant. proteomics data | 2023

Curtain | exploration & sharing of MS-based proteomics data | 2023

MASH Native | native top-down proteomics | 2023

TeaProt | proteomics/transcript analysis with novel underrepresented PTM genesets | 2023

TurnoveR | calculates rates of protein turnover from MS proteomics | 2023

CNN-GNN | for MS ion encoding | 2023

Sequence Coverage Visualizer (SCV) | protein seq. coverage 3D visualization | 2023

TargetDecoy |QC for the Target Decoy Approach for peptide ident | 2023

OmicLearn | ML for biomarker discovery from proteomics and Omics data | 2023

CPPA | exploring proteomic & phosphoproteomic data in cancer | 2023

MS-DAP | analyzing & interpreting label-free proteomics datasets | 2023

MetaLab MAG | genome based metaproteomics | 2023

TopPICR | Top-Down proteomics data analysis | 2023

PrIntMap-R | viewing protein coverage in a quantitative manner | 2023

MetaProD | MS analysis for multiplexed proteomic & metaproteomic data | 2023

CaspSites | collection of human caspase substrates | 2023

MS Ana | identify peptides in tandem MS data using a library of previously identified spectra | 2023

BIRCH | used for reducing batch-effects in proteomics data | 2023

Scribe | now part of EncyclopeDIA, library searching for DIA| 2023

DATSIGMA | single-cell analysis using image-guided MS | 2023

pyAscore| Ascore algorithm for localizing PTMs | 2023

MZA | mass-to-charge (m/z) generic data storage & access tool | 2023

compareMS2 | global similarity between tandem MS datasets | 2023

MSFragger Search Engine |as a node in Proteome Discoverer | 2023

PeptideRanger | optimize synthetic peptide selection for MS | 2023

TheDeuteriumCalculator | hydrogen–deuterium exchange MS Analysis | 2023

HyPep | for identification of neuropeptides | 2023

MS-TAFI | analysis of fragment ions generated from intact proteins | 2023

typic | ranking of proteotypic peptides for targeted proteomics | 2023

MSstatsShiny | statistical analysis of quantitative proteomic data | 2023

psm_utils | utilities for parsing & handling peptide-spectrum matches | 2023

Crux | analysis of bottom-up tandem MS data | 2023

pmartR | QC processing, statistical analysis & vis of MS omics data | 2023

Tide | database searching for peptide identification from tandem MS | 2023

ANN-SoLo | fast & accurate spectral library search engine | 2023

AlacatDesigner | design of peptide concatamers for protein quantitation | 2023

CHalf | peptide intensity info within a denat curve to calculate denat midpoint of protein/peptide fragments | 2023

spectrum_utils | MS data processing and visualization | 2023

ProteomicsML | community-curated data sets & tutorials for ML in Proteomics | 2023

Cytoscape stringApp 2.0 | analysis & vis. of heterogeneous biological networks | 2023

Kojak | ident. of cross-linked peptides from MS | 2023

ProtView | in silico protease evaluation & selection in a proteomic context | 2023

Tissue / organelle specifc

Cell Cycle database (CCdb) | 2023

MetaMass | tool for meta-analysis of subcellular proteomics data | 2019

SubCons | ensemble method for improved human subcellular predictions | 2017

TissueNet | protein-protein interactions across human tissues | 2022

Human Plasma Proteome Project Data Central at Peptide Atlas | 2014

jMorp | proteome data for plasma from >5000 healthy Japanese volunteers | 2023

The Human Skin Atlas | 2023

Liverbase 2.0 | 2012

LiverWiki | 2017

HKUPP | Human Kidney & Urinary Proteome Project | 2016

Human Salivary Proteome Wiki | 2016

HipSci | human induced pluripotent ttem cell initiative | 2018

DeepMitoDB | predicted subcellular localization of mitochondrial proteins | 2020

MitoProteome | Human Mitochondrial Protein Database

MitoCarta 3.0 | inventory of mammalian mitochondrial proteins | 2020

MPIC | Mitochondrial Protein Import Components | 2014

Matrisome Project | normal & tumor extracellular matrices | 2020

MatrisomeDB | extracellular matrix (ECM)-protein knowledge database

HSPD | Human (Homo sapiens) sperm proteome Database

Human Transmembrane Proteome

Membranome | structural & functional data of bitopic transmembrane proteins

MolMeDB | database about interactions of molecules with membranes

HTP | resources of the a-helical human transmembrane proteins

MVsCarta | compendium of microvescicles protein components

MetazSecKB | human/animal secretomes plus other subcellular locations

COMPARTMENTS | subcellular localization database

TISSUES | tissue expression database

PredHSP | heat shock proteins & their class

iLIR | autophagy database for LIRCPs

Disease specifc

Alzbiomarker | Alzheimer biomarker measurements from cerebrospinal fluid & blood

Alzheimer's Disease Proteome Database

DAPD | Diabetes Associated Proteins Database

Inflammatory Bowel Disease | Multi'omics Database

BiomarkerBase | Amplion

DISEASES | Disease-gene associations mined from literature


Breast Cancer Proteome Portal | 2023

Cell Model Passports | preclinical cancer Models

caAtlas | immunopeptidome atlas of human cancer

MSpectraAI | decipher multi-tumour MS data using deep neural networks

QCPA | Quantitative Cell Proteomic Atlas

ProTargetMiner | proteomics signature library of anticancer molecules

OncoPPi Portal | network of cancer-associated protein-protein interactions

CellMinerCDB | exploration & analysis of cancer cell line pharmacogenomic data

cBioPortal | integration & analysis of CPTAC proteomics data

ProTargetMiner | proteome signature library of anticancer molecules

Leukemia Protein Atlases | AML (Adult, Pediatric), ALL (Pediatric)

dbDEPC3.0 | differently expressed proteins in human cancer

QPCA | panel of targeted assays profiling activation of pathways in cancer cells

Cancer DriverDB | the open database of cancer biomarkers

canSAR v2.0 | Integrated Cancer Drug Discovery Platform, CRUK

TCPA | The Cancer Proteome Atlas

NCI-60 Cancer proteome database

CPTAC | Clinical Proteomic Tumor Analysis Consortium

The CPTAC Assay Protal

TSNAdb | Database for Tumor-specific Neoantigens

P-MartCancer | analysis of shotgun cancer proteomic datasets

MCLP | functional proteomics of cancer cell lines

CanProVar | germline & somatic variations in the human proteome

MYCbase | Myc assocaited database

Colorectal cancer atlas | quant. & non-quant. protein expression data

Acute Myeloid Leukemia Protein Galaxy

TRGAted | survival analysis using protein data in the Cancer Genome Atlas

Genes associated with platinum resistance in cancer

PTM specific

CurtainPTM | exploration & sharing of MS-based proteomics PTM data | 2023

pyAscore | localizing peptide PTMs from MS data

multiFLEX-LF | quantify the PTM stoichiometries in label-free proteomics data sets

Phosphomatics | suite of tools for downstream analysis of MS global phosphoproteomics data

PHOSIDA | posttranslational modification database

Phospho.ELM | database of S/T/Y phosphorylation sites

PTMViz | analyzing & visualizing histone PTM data

PTM-Shepherd | characterization of PTM profiles detected in open searches

GAPP | proteogenomic profiling of PTMs in prokaryotes

motifeR | ident. & vis. of protein PTM motifs

ActiveDriverDB | human disease mutations in PTM sites of proteins

Machine learning empowers phosphoproteome prediction in cancers

PTMphinder | PTM site localization & motif extraction

UNIMOD | ~1500 protein modifications for MS

FAT-PTM | for examining post-translational modification data

PTM select | identify protease combos for optimal coverage of global or targeted PTMs

PTMiner | filtering, localization & annotation of protein PTMs

dbPTM | functional & structural analyses for PTMs

PTM-SD | Post Translational Modification Structural Database

PTMD | database of human disease-associated PTMs

iPTMnet | protein post-translational modifications (PTMs) in systems biology context

ModProt | post-translational modification map of proteome

PTMfunc | functional predictions for protein post-translational modifications

PIPI | PTM-Invariant peptide identification

TagGraph | PTM identification from high-quality tandem mass spectra

PTMscape | tool to predict generic PTMs & map hotspots of mod. X-talk

VPTMdb | a viral PTM database

Peiman | enrichment analysis in post translational modification (PTM) types


Scop3P | human phosphosites within their full context

Phosphopedia | human phosphorylation sites (>100,000) & phosphopeptides

Phopepmass | db & search assisting human phosphorylation peptide ident. from MS

phospho (ssGSEA) & PTM enrichment analysis (PTM-SEA)

qPhos | database of protein phosphorylation dynamics in humans

PhosFate | analysis of human quantitative phosphoproteomics data

EPSD | euraryotic phosphorylation site database

PhosphoSitePlus | online resource of PTMs - phosphoryl, ubiquitin, acetyl & methylation

PhoSigNet | systematic resource for phosphorylation mediated signaling network

DAPPLE 2 | PTM sites using data for 19 different PTMs from 16 databases

CPhos DB | identify evolutionarily conserved phosphorylation sites

PhosphoPath | visualization & analysis of quantitative phosphoproteome datasets

Selphi | automated analysis of global phosphoproteomics datasets

GPS 5.0 | prediction of Kinase-specific Phosphorylation Sites

iEKPD 2.0 | eukaryotic kinases, phosphatases & proteins w/ phospho-p-binding domains

Quokka | prediction of kinase-specific phosphorylation sites in the human proteome

HisPhosSite | histidine phosphorylated proteins & sites

Prospect | predict protein histidine phosphorylation sites in bacteria

predPhogly-Site | phosphoglycerylation sites by incorporating probabilistic seq-coupling


UbiBrowser 2.0 | known & predicted ubiquitin ligase/deubiquitinase–substrate interactions

DeepUbi | deep learning framework for prediction of ubiquitination sites

DeepNitro | prediction of nitration & nitrosylation sites by deep learning

GPS-PAIL | prediction of internal Lysine acetylation

iSuc-PseAAC | predicting Lysine succinylation in proteins

GPSuc | generic & species-specific succinylation sites prediction

SuccinSite | Succinylation site prediction

HybridSucc | general & species-specific Succinylation Site Prediction

SwissPalm | protein S-palmitoylation database

SVMyr | prediction of protein G-myristoylation sites

DeepCSO | prediction tool for recognition of Cysteine S-sulphenylation sites

SIMLIN | multi-stage ensemble learning model for S-sulphenylation prediction

MDD-SOH | web server for identifying S-sulfenylation sites

PRmePRed | protein arginine methylation prediction tool


pGlyco3 | analysis of intact glycopeptides & modified glycans

MS-Decipher | database search for deciphering spectra of O-linked glycopeptides

O-GlcNAcAtlas |a database of experimentally identified O-GlcNAc Sites & proteins

GlyGen | computational & informatics resources for glycoscience

N-GlyDE | N-linked glycosylation site prediction

Glyco-DIA | quant. O-glycoproteomics w/ silico-boosted glycopeptide libraries

N-GlycositeAtlas | DB for MS human N-linked glycoprotein & glycosylation site mapping

GlycoPat | shotgun glycoproteomics data analysis

GlycoSiteAlign | selectively aligns amino acid sequences around glycosylation sites

Glypy | open source glycoinformatics library

GlyTouCan | the glycan repository

PepSweetener | manual annotation of intact glycopeptide MS spectra

UniCarbkb | knowledge platform for glycoproteomics

GRITS | annotation of glycomics MS data

GlycoPep DB | assign glycan comp. to MS data of glycopeptides

LaCyTools | data processing for analysis of LC-MS glycoproteomics data

GlycoPep ID | assign peptide comp. to CID data of glycopeptides

DecoyDeveloper | on-Demand, de novo decoy glycopeptide generator

GlycoPep Evaluator | generate decoy glycopeptides & score ETD data


MoFi | annotating glycoprotein mass spectra by integrating hybrid data

GlycoMine | machine learning approach predict. N-, C-, O-link glycosyl.

NetOglyc | neural network predictions of mucin type GalNAc O-glycosylation

O-Glyco proteome DB (Human)

Glycodomain | visual representation of glycosylated proteins

GlycoDigest | a tool for exoglycosidase digestions

CAZy | Carbohydrate-Active enZYmes Database


STRAP PTM | Software for Differential Comparison of PTMs

Organsim specifc

TaxIt | untargeted strain-level ident. using MS/MS spectra from pathogenic samples

PathRings | exploration of ortholog & expression data

OrthoDB | hierarchical catalog of orthologs

OMA | orthology database

InParanoid | ortholog groups with inparalogs

OrthoInspector | package dedicated to orthology inference & analysis

EggNOG | nested orthology inference across 3686 organisms

PaxDb | protein abundance across organisms

PhosphOrtholog | PTMs on proteins orthologous across species

Proteny | tool to analyze synteny at the protein level

NOmESS | homology-driven assembly of NOn-redundant protEin Sequence Sets

--- | excellent list of orthology databases


ViPTree | the Viral Proteomic Tree server

HIV mutation browser


µProteInS | for finding novel bacterial microproteins

MCPdb | bacterial microcompartment database

psortB | bacterial localization prediction tool

SecretP v2.1 | proteomic analysis of Gram-negative bacterial secreted proteins

MimicMe | predicts host-like proteins (mimics) in pathogenic organisms

CodaChrome | bacterial proteome comparison with GenBank finished bacterial genomes

PVCbase | resource for the PVC bacterial proteomes

STEPdb | DB of sub-cellular topology & localisation of the E.coli polypeptides

EcoCyc | E. coli K-12 database

EcRBPome | database of all known E. coli RNA-binding proteins

SubtiWiki | integrated database for the model organism Bacillus subtilis

CHOPIN | database of models of Mycobacterium tuberculosis (Mtb)

SecProMTB | secretory proteins in Mycobacterium tuberculosis

AureoWiki | integrated database for Staphylococcus aureus

LeptoDB | genomic & proteomic data of 23 Leptospira species

VectorBase | invertebrate Vectors of Human Pathogens

PBIT | pipeline builder for ident. of drug targets for infectious diseases


EuPathDB | genomic & other datasets associated with diverse eukaryotic microbes

CYCLoPs | protein abundance & localization changes S. cerevisiae

YeastRGB | comparing, abundance, localization, of yeast proteins across cells & libraries

LoQAtE | localization & quantitation atlas of the yeast proteome

FPD | fungi phosphorylation database

Secretool | fungi

PlantMWpIDB | MW & isoelectric point of proteins from plant species

Plant PTM Viewer

Plant-PrAS | physicochemical, structural properties & novel functional regions

PPDB | Plant Proteome DataBase for A.thaliana & maize

PlantPepDB | manually curated plant peptide database

Arabidopsis thaliana Seed Proteome

Arabidopsis PeptideAtlas

Arabidopsis | SUBA3 subcellular localisation DB

Arabidopsis | ASURE subcellular reference portal

Arabidopsis | protein-protein interactions viewer

PTIR | predicted tomato interactome resource

SpirPro | spirulina proteome repository

PlantPReS | plant proteome response to stress

CannabisDraftMap | cannabis draft proteome


TriTrypDB | incl. MS data for Trypanosoma brucei, cruzi & leishmania

TrypsNETDB | protein interactions for trypanosomatid parasites

PlasmoDB | plasmodium - a bit of proteomics embedded

PvaxDB | structural repository of Plasmodium vivax proteome


Worm PES | C. elegans database resource

iProteinDB | PTMs in Drosophila species

DPAV | drosophila proteome atlas viewer

ProtoBug | hierarchical classification of insect proteomes

KAIKO 2DDB | 2D PAGE database for analysis of silkworm proteins


ProteINSIDE | proteomics data from ruminants via orthologs

BoMiProt | database of bovine milk proteins


DiagnoTop | discriminating bacterial pathogens without database search

ProteoClade | taxonomic-based annot. & quant. of bottom-up proteomics data

OceansMap | data sharing platform for ocean metaproteomics data

pepFunk | peptide-centric functional analysis in metaproteomic human gut microbiome

mPies | tool for creation of protein databases & auto protein annotation

ProteoStorm | ultrafast metaproteomics database search

MetaProteomeAnalyzer (MPA) | analyze & visualize metaproteomics (& proteomics!) data

MetaLab | automated pipeline for metaproteomic data analysis

MetaProteomeAnalyzer | analyze & visualize metaproteomics (& proteomics!) data

Metagomics | peptide-centric functional & taxonomic analysis of metaproteomics data

Sysmo-DB | Systems Biology for Micro-Organisms

UniPept | functional analysis of metaproteome data

MetaProSIP | inference of elemental fluxes in microbial communities

MP3 | prediction of pathogenic proteins in metagenomic & genomic datasets

Blazmass | proteomic search engine with ComPIL integration for metaproteomics

MAPLE | Microbiome Analysis PipeLinE for human gut metaproteomics

Cobia | prediction & consequences of cofragmentation in metaproteomics

Mass Spec Tools

HowDirty | assesses the level of contamination of LC-MS results | 2023

einprot | workflows for statistical analysis of quant. proteomics data | 2023

Curtain | exploration & sharing of MS-based proteomics data | 2023

HUMOS | how to understand my Orbitrap Spectrum?

MMseqs2.0 | ultra fast & sensitive protein search & clustering suite

Skyline | MacCoss Lab Software - targeted proteomics environment

......Percolator | peptide identification from shotgun proteomics datasets






......Population Variation


......Proteotypic Peptide Viewer




......Avant-garde | refining DIA (& PRM) through control of the FDR

......PiNET | downstream analysis & visualization of proteomics data

MS2PIP | predicts fragment ion peak intensities

SRM Atlas


......DeepMass:Prism | deep learning package

......Perseus | shotgun proteomics data analyses

......EBprotV2 | diff. protein abundance analysis of labeling-based quantitative data

......LFQ-Analyst | interact. web-platform to analyze & visualize MaxQuant data

MaxQB | The MaxQuant DataBase

ProteomeTools | project between TUM, JPT, SAP, Thermo

......Prosit | deep learning package

Heck Lab Software

......XlinkX - analysis of XL-MS data




Software Tools Developed at CCMS

......MSPLIT | spectral-library search for ident. of mixture spectra of up to 2 peptides

......MSPLIT-DIA | spectral-library search for ident. of mixture spectra of up to 10 peptides

......MixGF | stat. signif. of pept.-spectrum-matches for multiplexed MS/MS Spectra

......MS-GF+ | database search for peptide identification

P-Mart | analysis of ion abundance global proteomics data

FLEXIQuant-LF | quantify protein modification extent in label-free proteomics data

Matthew The




SpeCollate | deep cross-modal similarity network for MS data based peptide deduction

mokapot | fast, flexible semisupervised learning for peptide detection

DO-MS | data-driven optimization of MS methods

DDAMSProteomics | a quantitative MS proteomics analysis pipeline in NextFlow

TPP | Trans-Proteomic Pipeline collection of integrated tools for MS/MS proteomics

SWATHProphet | software tool for analysis of SWATH (DIA) data

WinProphet | create, edit, manage, & execute proteomics pipelines based on TPP

StPeter | label-free quantification on shotgun MS/MS spectra

phpMs | a PHP-Bbased MS utilities library




PepFormer: Predict & Enhance Peptide Detectability Based on Sequence Only

Proline | software suite for large-scale proteomics

proDA | protein differential abundance for label-free MS

MetaMSD | meta analysis for MS data

PepFoot | semiautomated processing of protein footprinting data

SanXoT | build workflows for quant. h-t-p proteomics & statistical analysis

pFind Studio | computational solution for MS-based proteomics

......pNovoM | for mirror protease deNovo sequencing

PD-Nodes | collection of nodes for Thermo Scientific Proteome Discoverer

DeepMSPeptide | peptide detectability prediction using deep learning

mzCloud | mass spectral database

FragPipe | GUI for running MSFragger & Philosopher

MSFragger PD-nodes | fragment-ion indexing for peptide ident. & proteomic search

protti | data analysis of peptide- & protein-centric bottom-up proteomics data

Philosopher | complete toolkit for shotgun proteomics data analysis

ProteoCombiner | integrating bottom-up with top-down data

TIMSconvert | conversion of raw data from Bruker timsTOF Pro, fleX, & SCP MS

FragmentLab | peptide frag. spectra in detail & convert RAW files to MGF

PINT | store, query, & visualize large proteomic experiment results

IceR | quantitative label-free proteomics workflow

MetaNovo | probabilistic approach to peptide & polymorphism discovery in MS datasets

RAId | peptide scoring & statistical methods for tandem MS data with

COSS | tool for spectral library searching

pClean: preprocess high-res. tandem MS for db searching

ANN-SoLo | spectral library search engine for open modification searching

Picky | method designer for targeted proteomics (SRM & MRM)

Purple | method designer for targeted viral proteomics

OpenMS | offers data structures & algorithms for processing of MS data

......Epifany | efficient Bayesian protein inference

......OpenPEPXL | protein-protein cross-link identification

......MHCquant | identify & quantify peptides from MS raw data

......FLASHDeconv | ultrafast deconvolution for top-down proteomics

ProtyQuant | comparing label-free shotgun datasets using accu. peptide probs

Phoenix Enhancer | for proteomics data mining using clustered spectra

PACOM | Java tool to visualize & compare large proteomics datasets

ProHits | info management & analysis of MS data with focus on interaction proteomics

UCSF ProteinProspecter | tools for mining sequence databases

Morpheus | 5 times faster than OMSSA for large human datasets

Pecan | peptide detection directly from DIA data without the need of a spectral library

Crux | analysis tools for interpreting protein MS data

MS2-Deisotoper | deisotoping high-resolution MS/MS spectra

BioInfra.Prot | 'free' proteomics analysis consulting services

Scavager | validation algorithm based on gradient boosting for shotgun proteomics

PAnDA | MacCoss lab - post analysis data aquisition

Peptide-Shaker | interpretation & identification results from multiple search engines

CharmeRT | ident. & valid. of chimeric spectra using retention time prediction

SearchGUI | config. & run proteomics ident. search engines & de novo seq. algorithms

IdentiPy | search engine for shotgun proteomics in Python

SafeQuant | analysis of quantitative (LFQ,TMT,HRM) proteomics data

proteiNorm | normalization & analysis of TMT & Label-Free protein quant.

Falcon | large-scale tandem MS clustering using fast nearest neighbor searching

msCRUSH | mass spectral clustering using locality sensitive hashing

ProCon | conversion of commercial formats to mzIdentML 1.1 & PRIDE XML

TOMAHAQ | triggerd offset, Mmultiplexed, acc. mass, high-res., abs. quantification

MSREDUCE | ultrafast reduction of big MS data

NIST | Mass |& Fragment Calculator Software

MaConDa | MS Contaminants Database


RobNorm | normalization method for labeled quantitative MS

OptiMissP | missingness in proteomic DIA MS

......OptiMissP | shiny app

obaDIA | analysis pipeline for quantitative proteomics data

Prostar | differential analysis of quantitative proteomics data

Proteus | R package for downstream analysis of MaxQuant output

Deuteros | analysis & visualization of differential hydrogen deuterium exchange-MS

DECA | Deuterium Exchange Correction & Analysis

RawTools | scan data parsing & quantification, QC of Thermo Orbitrap raw MS files

Informed Proteomics | algorithms for proteomic MS data analysis

iPQF | iTRAQ (& TMT) Protein Quantification based on Features

ProteoSign | protein differential expression analysis

ProteomeGenerator | de novo transcriptome assembly & peptide mass spectral matching

Mass-up | MS utility for proteomics

IPSA | interactive peptide spectral annotator

Picky | simple method designer for targeted proteomics

ReDU | framework to find & reanalyze public MS data

Protalizer | automated DIA proteomics data analysis

SpecOMS | all-to-all MS spectra comparisons within minutes

HiQuant | rapid analysis of large-scale MS protein quantification data

Crux | software toolkit for tandem MS analysis

PepExplorer | similarity-driven tool for analyzing de novo sequencing data

SWATH Atlas | analysis of generated MS data libraries

TopFind | knowledgebase & analysis resource for protein termini & protease processing

Peptracker | tools for management, vis. & analysis of quantitative information

pyQms | generalized, fast & accurate MS data quantification

PeptideTracker | storing of info on protein concentrations in biological tissues

PBLMM | Peptide-based linear mixed models for diff. exp. analysis of shotgun proteomics

ProLuCID | fast, sensitive tandem MS-based protein identification program

EasyProt | complete graphical platform for analysis of MS/MS data

MSpC | spectral count based label-free quantitative proteomics

Peptagram | converts proteomics data into HTML5 vis.

Toffee | highly efficient, lossless file format for DIA-MS

protExpress | protocol data management & XAR file creation

STRAP PTM | differential comparison of PTMs

ThermoRawFileParser | takes a thermo RAW file as input & outputs a metadata file


......IPeak | peptide ident. pipeline (ProteoAnnotator)

mzXML Plotter & Plotly

mms2plot | visualizes multiple MS/MS or MS2 for mod &/or non-mod. peptides

ProtBase | Arizona Cancer Centre

msproteomicstools | python module for MS-based proteomics

protk | proteomics toolkit - command line tools in Ruby

MSstats | statistical tool for quantitative MS-based proteomics

Eatomics | shiny exploration of quantitative proteomics data

SpliceVista | splice variant analysis in shotgun proteomics data

SpliceProt | repository of human, mouse & rat alternative splicing transcripts translated in silico | 2014

RCPA | proteomics tools

HiTMaP | informatics toolbox for Maldi-imaging proteomics

GeenaR | reproducible MALDI-TOF Analysis

MALDIquant | quantitative analysis of MALDI MS data

pDeepXL: MS/MS Spectrum Pred. for X-Linked Peptide Pairs by Deep Learning (.zip)

MS Annika | X-linking search for use with cleavable X-linkers & MS2 spectra

xiView | vis. of cross-linking/MS data

xiNET | vis. of cross-linking/MS data

xiSPEC | auto. spectra annot., intuitive interac., easy testing of hypoth., export for public.

xiQ | minimalistic software for precursor ion quantitation

mzTab | reporting MS-based proteomics & metabolomics results

MSqRob | robust statistical inference for quantitative LC-MS proteomics

padua 0.1.8 | Python interface for Data Analysis with MaxQuant & Perseus

ProVision | analysis of proteomics data processed by MaxQuant

ProteoSuite | analysis of quantitative MS data

seaMass | sparse signal restoration for MS

GIRO | groupwise image registration & normalisation

TRIC | graph-based alignment software for SRM or SWATH-MS

GOAT | optimize LC gradients in shotgun proteomics exp.

Streaming vis. of LC-MS raw data & results

MiST | MS interaction STatistics - scoring of affinity purification-MS data

PASS | protein assembler with [very] short sequence peptides

M2Lite | converts msf files to standard mzIdentML format

iMonDB | auto extract, store, manage MS instrument parameters from raw data files

PatternLab | tool(s) for analyzing shotgun proteomic data

Mapsy | python library for MS proteomics data analysis

MzJava | analysis of large scale proteomics & glycomics MS data sets

QCQuan | analyses labeled LC-MS/MS proteomics diff. expression exp.

LogViewer | QC metrics for LTQ-FT & LT-Orbitrap instruments

rapid NOVOR | fast MS spectra protein identification program

PAnalyzer | software tool for protein inference in shotgun proteomics

HiXCorr | high-speed XCorr engine for high-res. spectra

pView | LC-MS/MS Data Viewer & Analyzer

JAMSS | a GUI Java MS Simulation Suite

MSAcquisition Simulator | data-dependent acquisition simulator

ProSight Lite | matching single candidate protein sequences & modifications

DeuteRater | kinetic curves for deuterated water labeled proteins

Ursgal | Python module - bottom-up proteomics for large-scale analysis

pValid | beyond target-decoy approach in shotgun proteomics

SAAS | Search All, Asses Subset strategy for FDR estimation in shotgun proteomics

ProteoModlR | R Suite for Quantitative Proteomics Pathway Modeling

iMPAQT | a tool for analysis of MRM chromatograms

Neo-pep-tool | neopeptide discovery in proteomics data

pyproteome | package for managing proteomics data

Curatr | creating, curating, & sharing a mass spectral library

Genoppi | integrative analysis of proteomic data & genetics

Mzmine | MS data processing with main focus on LC-MS data

MSCypher | improved ident rates & quant of low abundant peptides & proteins

DeconTools (Decon2LS) | detecting features in MS data by using the isotopic signatures

QuiXoT | quantification & statistical analysis of MS proteomics

MetaMorpheus | label-free quantification algorithm with PTMs for MS proteomics

FlashLFQ | ultrafast label-free quantification algorithm for MS proteomics

StatQuant | to analyze quantification data from MS experiments

NSAF | approach for using spectral counting in quantitative proteomics

UniNovo | universal tool for de novo peptide sequencing

DecoyPYrat | fast non-redundant hybrid decoy sequence generation

Sfinx | straightforward filtering index for AP-MS data analysis

MaSS-Simulator | MS/MS simulator for generating test datasets for big data algorithms

UV-POSIT | structural interpretation of ultraviolet photodissociation (UVPD) Mass Spectra

EpiProfile2.0_Family | processing epi-proteomics MS Data

ProSave | restoring quant. data to manipulated subsets of protein lists

Biosaur | for LC–MS peptide feature detection with ion mobility support

moFF | modest Feature Finder to extract MS1 intensities from Thermo raw file

R.I.D.A.R | filters MS1 scans of MGF file for reporter ions

msXpertSuite | incl. mineExpert for MS1 data visualization

Param-Medic | improving MS/MS DB Search Yield by Optimizing Parameter Settings

PeptideProphet | validates peptide assignments to MS/MS spectra

DIA-Umpire | computational analysis pipeline for DIA proteomics data

DIAlignR | R package for alignment of DIA mass-spec data

MS Data Miner | analyze, process, validate, compare, display files from MS software

MSSuite | ProteoStats

IQuant | pipeline for quant. proteomics based upon isobaric tags

IsoProt | pipeline to analyse isobarically labelled MS based quant. proteomics data

Multi-Q2 | isobaric labeling quantitation analysis with improved accuracy & coverage

APP | automated proteomics pipeline

EXIMS | new peak picking method for EXploring Imaging MS data

MassWiz | novel scoring algorithm with target-decoy analysis pipeline for tandem MS

mapDIA | model-based analysis of quantitative data in DIA-MS

Ionbot | searches MS2 spectra against a concatenated target/decoy protein database

MS & proteomics data analysis

RforProteomics | add package to 'Using R & Bioconductor for proteomics data analysis'

psims | for writing XML documents for HUPO PSI-MS mzML & mzIdentML

mzR | parser for netCDF, mzXML, mzData & mzML & mzIdentML files

MSnbase | plotting, data manip. & processing of MS proteomics data

pRolocGUI | interactive vis. of spatial proteomics data

pRoloc | pattern recognition on quant. MS data to infer protein sub-cellular localisation

Synapter | reanalysis of label-free proteomics data acquired on a Synapt G2 MS

StatsPro | approaches for detecting diff. expression in label-free quant. proteomics

msmsTests | statistical tests for label-free LC-MS/MS data by spectral counts

msmsEDA | exploratory data analysis of LC-MS/MS data by spectral counts

Isobar | anal. & quant. of isobarically tagged MSMS proteomics data

SPEQ | quality assessment of peptide tandem mass spectra

SynthQA | Hierarchical Machine Learning-based Protein Quality Assessment

r-ptxqc | QC reports for shotgun LC-MS data analyzed with MaxQuant software

pmartR | QC processing of MS omics data, in particular proteomic data

proteoQC | R package for proteomics data quality control

MSnID | explor. & assess. of confidence of LC-MSn identif.

specL | peptide spectrum matches for use in targeted proteomics

PCprophet | protein complex prediction & differential analysis

MSBayesPro | bayesian protein inference for LC-MS/MS proteomics

ProteinART | protein inference solutions

Anubis | automated peptide detection & Quantification in SRM data

ProteoCombiner | bottom-up & top-down proteomics to improve proteoform ident.

hmSEEKER | identification of hmSILAC doublets in MaxQuant output data

Dart-ID | retention time alignment & peptide identification confidence updates

iq | relative protein abundances from ion quantification in DIA-MS

ncGTW | targeted realignment of LC-MS Profiles

GproDIA |DIA glycoproteomics with statistical control

DiaLib | generation of theoretical ion library of peptides & glycopeptides for DIA

msImpute | methods for MS label-free proteomics imputation

PB-Net | peak integr. by sequential deep learning for MRM

Toffee | highly efficient, lossless file format for DIA-MS

PolySTest | statistical testing of proteomics data with missing values

Top-Down specific

MASH Native | native top-down proteomics | 2023

TDFragMapper | evaluating experimental parameters in top-down proteomics

FLASHDeconv | high-quality feature deconvolution for top-down proteomics

IMTBX | 2D signal extraction tools ion mobility-MS

Grppr | 2D isotopic grouping applied to LC-MS or IM-MS datasets

Top-Down Garbage Collector | select high-quality top-down proteomics spectra

TopPIC Suite


iTOP-Q | top-down proteomics Quantitation using XIC abundances

IMTBX + Grppr | top-down proteomics utilizing ion mobility-MS

MASH Explorer | processing of top-down high-resolution MS data

Software Tools Developed at CCMS

......MS-Deconv | deconvolution of top-down spectra

......MS-Align+ | top-down protein identification based on spectral alignment


CutDB | a proteolytic event database

CaspDB database

MitoFates | predicts mitochondrial N-terminal localization signal cleavage position

via Commercial

ThermoFisher - Proteome Discoverer

ThermoFisher - ProSightPC (Top-Down)

Bruker - ProteinScape

Waters - Progenesis QI

Sciex - ProteinPilot

Proteome Software | products

......Scaffold DDA | DDA Labeled & Label-free Quantitative Analysis

......Scaffold DIA | DIA analysis of proteomics experiments

......Scaffold 5 | DDA MS/MS Proteomics Tool

......Scaffold PTM | Protein Post Translational Modifications

Matrix Science - Mascot

Biognosys - Spectronaut

Bioinformatic Solutions - PEAKS

Protein Metrics - Byonic

Rapid Novor - Antibody sequencing

Mass Dynamics

Optystech - Pinnacle / Bolt

Premier Biosoft - ProteoIQ

InDigestion App (iOS)

Visualisation Tools

Venny 2.1 | venn diagram generator

VIQoR | visually supervised protein inference & protein quant.

Fiscore | protein structural data vis. & exploration

MS_Piano | annotating peaks in MS of peptides & N-glycopeptides

VIQoR | visually supervised protein inference & protein quant.

BLUR | protein divergences at whole proteome level between species

dagLogo | visualizing conserved amino acid sequence patterns in groups

Data-to-Viz | leads to most appropriate graph for your data

DEqMS | statistical testing of differential protein expression

DynOmics | computing & visualizing biomolecular systems dynamics

DrawAlignR | across run chromatogram alignment visualization

ShinyOmics | collaborative exploration of omics-data

PaintOmics 3 | for pathway analysis & visualization of multi-omics data

iNetModels | interactive visualization & database of multi-omics data

Omics Playground | visual analytics platform for multi-omics data

MOFA | Multi-Omics Factor Analysis

vMS-Share | NIST MS visualization & data mining repository

Cytoscape | platform for visualizing molecular interaction networks & biological pathways

Cytoscape apps | a complete range of addons for Cytoscape

PathBank | pathway database for model organisms

PathVisio | Biological pathway creation & curation

ComPPI | compartmentalized protein-protein interaction database

Proteinarium | Multi-Sample PPI Visualization & Analysis

Proteinarium 2 | Multi-Sample PPI Visualization & Analysis

Instant Clue | interactive analysis & vis. of scientific of data

PDV | an integrated proteomics data viewer

ontoFAST | semi-auto annotation of characters with biological ontologies

GiaPronto | graphical interpretation & analysis of proteins & Ontologies

ProtSpaM | fast alignment-free phylogeny reconstruction of whole-proteome sequences

ProtVista | renders position-based annotations for protein sequences

Protter | interactive protein feature visualization

VisioProt-MS | interactive 2D maps from intact protein MS

MhcVizPipe | QC Software for small to large-scale immunopeptidome data sets

Peptigram | peptidomics data vis.

PANDA-view | multiple vis. methods

ProteomeVis | protein properties from structure to sequence evolution across proteomes

CIG-P | circular interaction graph for proteomics

OmicsVolcano | interactive exploration of high-throughput biological data

VolcaNoseR | exploring volcano plots

msVolcano | dynamic volcano plotting for MS data

JSparklines | visualize numbers in Java tables

ProteoViz | analysis & visualization of Phosphoproteomics data sets

pViz.js | visualization of protein sequence features

BioJS | viewer for protein sequence features

Scop3D | visualization of sequence variation of a protein on its structure

DeepPrime2Sec | protein secondary structure prediction from primary sequences

DOSE | disease ontology semantic & enrichment analysis

TAPIR | visualization software for chromatographic data obtained by MS

NOVA | analysis complexome profiling data

Multiplierz | managing proteomic MS workflows & data analysis

DataShop | data vis., exploration & analysis

BatMass | MS data visualization

CLMSVault | protein X-linking MS data analysis & visualization

Clustergrammer | for visualizing & analyzing high-dimensional data

simplifyEnrichment | clustering & visualizing functional enrichment

InterMine | integrates biological data sources, for easy query & analysis

MS-Helios | a circos wrapper to visualize multi-omic datasets

YASARA | molecular-graphics, modeling & simulation program

OSPREY | computational structure-based protein design

Solubis | identify mutants that decrease protein aggregation tendency

iCOBRA | compare & visualize performance of methods for estimation or classification

MSviz-ui | the all purpose visualization app for MSViz

ProteoMill | network-based functional analysis portal for proteomics data

VANTED | visualization & analysis of Networks containing Exp. Data

MALDIViz | quality checks, visualizations & analysis of MS data

statTarget | signal drift correction & interpretations of quantitative MS

PseudoQC | regression‐based correction & normalization of complex proteomics datasets

QCMAP | performance diagnosis & prediction of LC-MS Systems

QC-Art | Dynamic, unsupervised QC methodology for MS

DeepQuality | MS QC via Compressed Sensing & Deep Learning

QCloud | quality control for MS-based proteomics labs

VSClust | variance-sensitive clustering of omics data

NetWheels | high quality peptide helical wheel & net projections

Icelogo | visualising conserved patterns in protein sequences

PlotsOfData | visualizes data & statistics to enable the comparison of experiments

Spot3D | visualization of sequence variation of a protein on its structure

BASILIScan | for the rational protein expression design

DisVis | visualize & quantify distance restraints between macromolecular complexes

Dynalogo | dynamic thresholding of matched quantitative proteomic microarray data


surfaltr | surface protein isoforms of transmembrane topologies

Metapredict V2 | predictor of consensus disorder & structure

prolfqua | proteomics differential expression analysis

ProSight Annotator | control & customization of protein entries in UniProt XML files

DeepTracer | de novo protein complex structure prediction from Cryo-EM Maps

kAAmer | protein database based on amino acid k-mers

FPocketWeb | protein pocket hunting in a web browser

Degronopedia | search degrons in proteomes of model organisms

ESIprot | charge state determination & MW for low res. ESI-MS

Quandenser | condenses quant. data from label-free MS experiments

HPAStain.R | cell type most associated with a set of proteins

psntools | protein structure network analysis

CKG | clinical knowledge graph to interpret clinical proteomics data

vcf2prot | personalized proteomes from VCF file & a reference proteome

Sequence Coverage Visualizer | protein sequence coverage 3D visualization

OMnalysis | analysis of quantitative transcriptomics & proteomics data

PeakBot | peak-picking in LC-HRMS profile mode data

MoSBi | signature mining for molecular stratification & subtyping

Blacksheepr | outlier analysis for pairwise differential comparison

POMAShiny | metabolomics & proteomics data analysis

ColabFold | prediction of protein structures & complexes

MSNovelist | de novo structure generation from mass spectra

PDBrenum | PDB files renumbered according to UniProt sequences

Foldseek | fast & accurate protein structure search

MP-NeRF | accelerating protein structure reconstruction from internal coordinates

Mechnetor | exploring protein mechanism & functional context of genetic variants

PARROT | recurrent neural network for analysis of large protein datasets

ProteinBERT | deep-learning model of protein sequence & function

Target-Decoy MineR | biological relevance of variables in noisy data sets

GNPS Dashboard | Collaborative Analysis of MS Data

PRYNT | prioritization of disease candidates from proteomics data

FunHoP | visualization & analysis of functionally homologous proteins

PredictProtein | resource for protein sequence analysis

InterMetalDB | Intermolecular Metal Binding Sites in Macromolecules

BatchServer | web Server for batch effect evaluation, visualization, & correction

ProteoSushi | annotate & quantify ptm, peptide-centric proteomics datasets

DescribePROT | amino acid-level protein structure & function predictions

Meltome Atlas | thermal proteome profiles across species or human cell lines/types

DisCovER | distance-based covariational threading for weakly homologous proteins

QDeep | Distance-based protein model quality estimation using deep ResNets

MAV-clic | management, analysis, & visualization of clinical data

GTO | toolkit to unify pipelines in genomic & proteomic research

MAP | model-based analysis of proteomic data

Verkstad | ToDO app, optimized for proteomics mass spec maintenance

psims | for writing XML documents for HUPO PSI-MS mzML & mzIdentML

gpGrouper | peptide grouping algo. for gene-centric infer. & quant. of bottom-up data

XINA | multiplexed proteomics kinetics data with network analysis

OpenProt | a modern view of protein translation

table of all published GWAS with proteomics data

NormalyzerDE | improved normalization of omics expression data

Panorama Public | repository of Skyline docs & data from published manuscripts

ProForma | a standard proteoform notation

DisEnrich | database of enriched regions in human dark proteome

DPD | Dark Proteome Database

ICBdocker | annotation of functional & structural features of proteomes

APPRIS | annotating principal splice isoforms

phosIDP | plots for visualizing intrinsically disordered proteins (IDPs)

DisProt | database of intrisically disordered proteins

Disorder Atlas | descriptive statistics interpretation of intrinsic disorder predictions

QUARTER | quality assessment for the putative intrinsic disorder in proteins

BASILIScan | analysis of intrinsic disorder patterns in homologous proteins

*** DisCons | quant. investigating conservation of protein disorder at the amino acid level

MobiDB | a database of protein disorder & mobility annotations

DFLpred | prediction of disordered flexible linker

MissingProteinPedia | to collate 'Missing proteins' defined by neXtProt

Taverna | domain-independent scientific workflow management system

DeNovoGUI | GUI for PepNovo+, DirecTag, pNovo+ (beta) & Novor (beta)

SEDA | for processing FASTA files containing DNA & protein sequences

Fasta-O-Matic | sanity check & if needed reformat FASTA files

DBToolkit | processing protein databases for peptide-centric proteomics

moCluster | multiple omics data integration & gene set analysis

MI-PVT | systematic visualization of proteins in human chromosomes

YPED | Yale protein expression database

STATegraEMS | the experiment management system for -omics

PIQMIe | semi-quantitative proteomics data management & analysis

MS-EmpiRe | peptide-level noise distributions for detection of diff. abundant proteins

ProteomeScout | repository & analysis resource for PTMs & proteins

PepQuery | peptide-centric search engine for novel peptide searching

CrossCheck | open-source, high-throughput database analysis software

Pyteomics | Python tools to handle various sorts of proteomics data

PyPDB | PDB search, data retrieval including BLAST & sequence motif queries

PSSMSearch | discovery of novel protein motifs (SLiMs, mORFs, miniMotifs) & PTM sites

Meme Suite | motif based sequence analaysis tools

MassTodonPy | estimate products of ETD in MS

Spada | splicing directed functional changes of the proteome

DOGMA | proteome & transcriptome quality assessment

PASS | a proteomics alternative splicing screening pipeline

SLiMAn | exploring Short Linear Motif-Mediated Interactions in Interactomes

ShettiMotif | search engine for short linear motifs / domains (SLiM)

EPD | characterising proteome dynamics in both human cells & model organisms

CABRA | cluster & annotate blast results algorithm

SignalP 5.0 | presence & location of signal peptide cleavage sites

Punchline | identifying & comparing Pfam protein domain differences

Surfacegenie | effective prioritization of candidate cell-type specific markers

CRAPome | contaminant repository for affinity purification

MoonProt | database of moonlighting proteins

IdentPMP | identification of moonlighting proteins in plants

MoonDB | predicted EMF proteins & set of manually curated moonlighting proteins

DextMP | moonlighting protein prediction by deep dive into text

TOPPR | stores high quality processed events for protease data

iProt-sub | in silico prediction of protease substrates & their cleavage sites

iHPDM | in silico human proteome digestion with peptide analysis & graphical vis.

ProteaseGuru | in silico tool for the planning of bottom-up proteomic exp.

Proteasix | predict proteases involved in naturally occurring peptide generation

Mechismo | mechanistic interpretations of structural modifications

Proteo3Dnet | integration of structural info with interactomics data

ComplexBrowser | ident. & quant. of protein complexes in large scale datasets

BioPlex | biophysical interactions of ORFeome-based complexes

NetProt | complex-based feature selection

CDB | heterodimeric protein complexes

CORUM | comprehensive resource of mammalian protein complexes

PEPPI | extraction of predicted protein-protein interactions

PSINDB | Postsynaptic PPI Database

PPIDomainMiner | inferring DDIs (Domain-Domain) using multiple sources of PPIs

UniReD | UniProt-Related Docs analyses biomedical literature to extract known PPIs

ProHits-viz | analyzing & visualizing screens & PPI data

PINOT | intuitive resource for integrating PPIs

APID | PPI experimental evidences & binary interactomes

HuRI | first complete reference map of the human PPI network

SAINT | Significance Analysis of INTeractome

Pickle | human direct protein-protein interactome database

STRING | protein-protein interaction database

DIP | Database of interacting proteins

DiffSLC | detection of essential proteins of a protein-protein interaction network

XLSearch | probabilistic DB Search Algo for Identifying Cross-Linked Peptides

LMPID | linear motifs mediated protein protein interaction database

PEP-SiteFinder | identify candidate protein-peptide interaction sites

GPS-Prot | data visualization for protein-protein interactions

Cross-ID: complex XL-MS driven protein interaction networks

HawkDock | structural prediction & analysis of protein-protein complex

Tabloid Proteome | database of public protein association networks

MaXLinker | identify cross-links from XL-MS data

InterPred | pipeline to identify & model protein-protein interactions

PPIExp | integration & visualization of PPI Data & Spatiotemporal Proteomics Data

MIEC-SVM | auto. pipeline for protein peptide/ligand interactions

SpotOn | determination of Hot-Spots at protein-protein interfaces

ECL | identification of cross-linked peptides using whole database

SLiMSuite | short linear motifs (SLiMs) in proteins as functional microdomains

Structure Mapper | finds homologous protein structures for amino acid sequences

Confold2 | contact-guided protein structure prediction tool

SELPHI | identification of kinase-assoc. networks from global phospho-proteomics data

Crescendo | identifies functional sites in proteins

Spotlite | co-complexed proteins

SFINX | filtering index for co-complex interactomics data analysis

PEPPER | find meaningful pathways/complexes

FunRich | functional enrichment analysis tool

INGA | prediction of protein function

PRINTS | compendium of protein fingerprints

ECOD | Evolutionary Classification of Protein Domains

ProteinCarta | termini tags from 9 organisms

PANOPLY | automated & reproducible proteogenomic data analysis

Spritz | proteogenomic database engine

Splicify | proteogenomic ident. of disease specific protein biomarkers from mRNA splicing

SMAP | pipeline for sample matching in proteogenomics

Proteome PheWAS browser | Pphenome-wide mendelian randomization mapping

PGMiner | complete proteogenomics workflow

pyGeno | python package for personalized proteogenomics

PGTools | analysis & visualization of proteogenomic data

Proteoformer | proteogenomic pipeline delineating true in vivo proteoforms

PPLine | proteogenomic pipeline for SAP/indels & alt. spliced variants discovery

MPC-bioinformatics | bacterial proteogenomic pipeline

Proteoform Suite | constructing, quantifying & visualising proteoform families

EVpedia | Extracellular Vesicles

pwOmics | pathway-based integration of time-series omics data using public DBs

RaftProt | Mammalian Lipid raft Proteome DB

XLink-DB | data storage & visualization for cross-linking data

Kojak | efficient ident. of cross-linked peptides in complex protein mixtures

ProXL | visualize & share protein Cross-linking Data

FunMod Network Analysis | Cytoscape Plugin

SW# | library for sequence alignment based on CUDA enabled GPUs

DAVID | DB for Annotation, Visualization & Integrated Discovery

NCIP/prot-express | GitHub

fLPS | fast discovery of compositional biases for proteins

ProGeRF | proteome & genome repeat finder tool

REP2 | detect common tandem repeats in protein sequences

customProDB | RNAseq to Fasta


OrthoDB software | compute orthologs on custom data

UniRep | deep representation learner for protein engineering informatics

PIA | Core-library

SUBAcon | max entropy justif. for Naive Bayes

aLFQ | R-package for estimat. abs. protein quant. from label-free LC-MS/MS data

Normalyzer | normalisation of omics datasets

THE-DB | comparative protein structure analysis of E. coli & human proteomes

*** BioQuery | Tool Discovery System

inmembrane | pipeline to predict if a protein is exposed on surface of bacteria

Zotero | Protein Gel Documentation System for Proteome Analyses

RAIN | automated image alignment for 2-D gel electrophoresis

S2P | processing of 2D-gel & MALDI-based MS protein data

ProteomeGRID | cluster image computing for Condor

pyProCT | cluster analysis for structural proteomics

RepExplore | technical replicate variance in proteomics data analysis

SIFTER | phylogeny-based protein function prediction

PhaSepDB | db of liquid-liquid phase separation related proteins

EBprot | bayesian analysis of labeling-based quantitative proteomics data

GProX | integrated analysis & visualization of large proteomics datasets

MSProGene | transcript databases for tandem MS search using RNA-Seq data

PrionW | identifies proteins with gln/asn rich prion-like domains

AutoDock | predicts how small molecules bind to a receptor

AutoDock Vina | molecular docking

GalaxyPepDock | Protein-peptide docking based on interaction similarity

pepATTRACT | docking protocol that is fully blind

SANSparallel | interactive homology search against Uniprot

RAPSearch2 | fast protein similarity search

EVcouplings | functional & structural info from evolutionary seq. record

PredSTP | SVM based model to predict seq. cysteine stabilized peptides

SEEK | sharing scientific datasets, models, simulations, processes & research outcomes

SplicePie | analyze non-sequential & multi-step splicing

Data Calibration | max. likelihood calibr. for samples quantified in batches

Hammock/Galaxy | clustering extremely large DBs of short peptide sequences

Hammock | clustering extremely large DBs of short peptide sequences with seq. motifs

DAVI | clustering & visualising protein domain architectures

Falcon@home | high through-put server for protein structure prediction

ProtSav | protein tertiary structure analysis & validation server

SIM-XL | identification of cross-linked peptides

PDID | protein-drug interaction database

DeepConvDTI | drug-target interact. via deep learning w/ convolution on protein seq.

Proteinator | drug leads based on secondary protein interactions

eFindSite | lig& binding site prediction & virtual screening

SecretP v2.0 | a new method for predicting mammalian secreted proteins

CP4P | FDR QC, control procedures & computing of adjusted p-values

ASAP | Amino-acid Sequence Annotation Predictor

SpectroGene | genome annotation using top-down MS

PrionW | identifies proteins containing gln/asp rich prion-like domains

MBPpred | prediction of membrane lipid-Binding Proteins

SEEK | psharing datasets,models or simulations, processes & research outcomes

hEIDI | to organize & manipulate large-scale proteomics data

ELASPIC | predicts stability effects of mutations on protein folding & interactions

GprotPRED | a tool for detection & classification of G-proteins

PDID | Protein-Drug Interaction Database in Structural Human-like Proteome

MODICT | mutation prediction tool based on 3D models

Hydrocalc | identify distinct characteristics of effector proteins

Epitopemap | visualising epitope predictions (currently MHC binding)for proteomes

qpMerge | Galaxy workflow for non-redundant set of quantifications for phospho-motifs

Dintor | functional annotation of genomic & proteomic data

proBAMsuite | genome-based representation & analysis of proteomics data

PPIP | identification of bioactive endogenous peptides

Pawer | protein array web explorer

protGear | protein microarray data pre-processing suite

arrayQualityMetrics | quality metrics report for microarray data

PMD | protein microarray database

MAPPI-DAT | PPI data generated from microarray-MAPPIT system

ArrayNinja | unifies planning, visualization, analysis of microarray experiments

Heatmapper | interactively visualize data in form of heat maps

FusionLearn | biomarker selection algorithm on cross-platform data

dbDSM | database of deleterious synonymous mutation

FASIL-MS | analysis scripts to quantify heavy-light acetylations

HydroCalc | hydropathy profiles calculated using Kyle-Doolittle scale

DISMS2 | direct proteome-wide distance calculation of LC-MS/MS runs

CombiROC | guided & interactive generation of multimarker panels

ProtCHOIR | proteome-scale generation of homo-oligomers

DLPacker | Prediction of Amino Acid Side Chain Conformations in Proteins

PiPred | deep-learning for prediction of p-helices

IonchanPred 2.0 | prediction of ion channel & their types

PyFolding | fitting kinetic & thermodynamic models to protein folding data

Apostl | analysis pipeline for affinity proteomics data

Aminode | amino acid evolutionary constrained analysis

Protein Parameters | similar to Expasy ProtParam tool

Aggrescan3D | prediction of aggregation propensity & protein solubility

Pon-Sol | effects of amino acid substitution on protein solubility

patcHwork | pH sensitivity analysis web server for protein sequences & structures

IPC | isoelectric point calculator

Proteome-pI | proteome isoelectric point database

PIP-DB | protein isoelectric point database

dbAMP 2.0 | database of antimicrobial peptides & relevant proteome data

PPIP | endogenous peptides identification with RNA-seq & MS2 data

qPortal | create, manage & analyze quantitative biological data

fuNTRp | random forest-based predictor to classify protein positions by type

PepFoot | semi-automated processing of protein footprinting data

FoldamerDB | a database of peptidic foldamers

GenesByMassSpec | identify genes based on mass spec. evidence


Additional software resources that may be worth looking at beyond those listed above can be found at |


HUPO-PSI | tools implementing mzIdentML

openMS | C++ library (+ python bindings) for LC/MS data management & analyses

The Barton Group | bioinformatics software tools

Unipept | proteomics tools from Ghent University

CCMS | software tools

SPC | Seattle Proteome Center & TransProteomic Pipeline

biospi Laboratory | tools for differential expression analysis in MS proteomics

Galaxy Training Material


BioDocker | repository for bioinformatics




Mybiosoftware | proteomics last updated 2022


Archive of sites/links that work but are considered too old |

2005_The UCSC Proteome Browser

2001_Superfamily 1.75

SuperPose | protein superpositions using a modified quaternion approach

Archive of sites/links that do not work but are kept for historical interest |

2021_HMPD | Human Mitochondrial Protein Database

2018_MitoMiner | Mitochondrial proteome

2018_Salivaomics | salivary omics database

2018_Hypo2 | a database of hypothetical proteins in humans

2018_SORFS.ORG | a repository of small ORFs identified by ribosome profiling

2017_SubCons | ensemble method for improved human subcellular predictions

2015_Caper 3.0 | Analysis of Chromosome-Centric Human Proteome Project Data Sets proteomic datasets

2015_CMPD | cancer mutant proteome database

2014_MitProNet | Mitochondrial proteome

2007_OrganelleDB | a database of organelle proteins, & subcellular structures/complexes

2006_YDPM | Yeast Deletion Proteomics of Mitochondria Databases

2004_PROWL | Rockefeller software tools

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