Databases
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 (resources@pastelbioscience.co.uk) 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 Old sites/links that no longer work are archived at the bottom of the page as a historical reference.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
.....ProteinExplorer
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
hu.MAP | Human Protein Complex Map
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
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
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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 (2023 = 133 so far) - no particular order
MFPPDB | multi-functional plant peptide database | 2023
OmicsSuite | analysis & visualization of multi-omics big data | 2023
CancerProteome| a database to decipher proteome landscape across various cancer types | 2023
Sage | fast proteomics searching & quantification at scale | 2023
CUDASW++4.0 | Smith-Waterman Protein Sequence Database Search *link broken | 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 sequence | 2023
Hefeweizen yeast | proteomic profiling across fermentation | 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 sequence-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 sequence | 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
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
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
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
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 sequences | 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
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 sequence 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
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
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
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
DISEASES | Disease-gene associations mined from literature
Cancer
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
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
Peiman | enrichment analysis in post translational modification (PTM) types
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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
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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
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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
Glycodomain | visual representation of glycosylated proteins
GlycoDigest | a tool for exoglycosidase digestions
CAZy | Carbohydrate-Active enZYmes Database
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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
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
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ViPTree | the Viral Proteomic Tree server
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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
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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
PlantMWpIDB | MW & isoelectric point of proteins from plant species
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 | 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
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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
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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
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ProteINSIDE | proteomics data from ruminants via orthologs
BoMiProt | database of bovine milk proteins
Metaproteomics
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
......BiodiversityPlugin
......MPPReport
......MS1Probe
......MSstats
......MSstatsQC
......Population Variation
......Prego
......Proteotypic Peptide Viewer
......Protter
......Quasar
......SProCoP
......Avant-garde | refining DIA (& PRM) through control of the FDR
......PiNET | downstream analysis & visualization of proteomics data
MS2PIP | predicts fragment ion peak intensities
......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
ProteomeTools | project between TUM, JPT, SAP, Thermo
......Prosit | deep learning package
......XlinkX - analysis of XL-MS data
......PhosphoDB
......RockerBox
......StatQuant
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
......Quandenser
......MaRaCluster
......Triqler
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)
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
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 dataCuratr | 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
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
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
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
MitoFates | predicts mitochondrial N-terminal localization signal cleavage position
via Commercial
ThermoFisher - Proteome Discoverer
ThermoFisher - ProSightPC (Top-Down)
......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
Bioinformatic Solutions - PEAKS
Rapid Novor - Antibody sequencing
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
Miscellaneous
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
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 PPIsAPID | 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
fLPS | fast discovery of compositional biases for proteins
ProGeRF | proteome & genome repeat finder tool
REP2 | detect common tandem repeats in protein sequences
OrthoDB software | compute orthologs on custom data
UniRep | deep representation learner for protein engineering informatics
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
SPC | Seattle Proteome Center & TransProteomic Pipeline
biospi Laboratory | tools for differential expression analysis in MS proteomics
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
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
