Databases
Presented are a number of links, in no particular order, to proteomic and protein databases as well as tools for Mass Spectrometry and Visualisation. These are currently mainly generic or associated with human biology and diseases but will be expanded in future to include other organisms. Please let Pastel BioScience know (resources@pastelbioscience.co.uk) of other databases that may be useful to the proteomics community.
Main Proteomics Databases
.....GlyConnect
.....Glycoforest
.....World-2D PAGE Constellation for gel-based 2D data
.....Pfam
.....InterPro
.....ProtVista
.....PDBe
.....PDBsum
.....IntAct
.....CATH
.....SCOP
.....SIFTS
.....EMPIAR
.....PIA
.....HMMER
.....Expression Atlas
.....Complex Portal
.....VarMap | DNA to protein mapping
UniProtR | retrieval in addition to screening visualization tool, & ID conversion
wwPDB | open access to high-quality 3D structural biology data
OMICSDI | linking public omics data sets w/ Omics Discovery Index
SORFS.ORG | a repository of small ORFs identified by ribosome profiling
.....Smorfs | FASTA files, generated from data provided by sorfs.org
.....ProteinExplorer
PIR | Protein Information Resource
CHESS | includes link to CHESS protein DB
hu.MAP | Human Protein Complex Map
SubCell BarCode | web portal to proteome subcellular localization
ProteomicsDB | DB using SAP HANA from Technische Universitat Munchen
.....HPAanalyze | R package to retrieve & analyze data from the HPA
CTPD | proteoform atlas from top down proteomics
TPB Home | the proteome browser
neXtProt | exploring the universe of human proteins
neXtProt - tools | peptide uniqueness checker
APPRIS | annotating principal splice isoforms
*** Caper 3.0 | to visualize chromosome-centric human proteomic datasets
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
Hypo2 | a database of hypothetical proteins in humans
MMseqs2.0 | ultra fast & sensitive protein search & clustering suite
EncoMPASS | Membrane Proteins Analyzed by Structure and Symmetry
SmProt | database of small proteins encoded by annotated coding & non-coding RNA loci
iProX | integrated proteome resources center in China
SAAVpedia | analysis pipeline to prioritize and interpret SAAVs
QCPA | Quantitative Cell Proteomic Atlas
*** PEDANT | Protein Extraction, Description and ANalysis Tool
Tissue / organelle specifc
OrganelleDB | a database of organelle proteins, & subcellular structures/complexes
MetaMass | tool for meta-analysis of subcellular proteomics data
SubCons | ensemble method for improved human subcellular predictions
TissueNet | protein-protein interactions across human tissues
Human Plasma Proteome Project Data Central at Peptide Atlas
jMorp | proteome data for plasma from >5000 healthy Japanese volunteers
*** Salivaomics | salivary omics database
HipSci | human induced pluripotent ttem cell initiative
HMPDb | Human Mitochondrial Protein Database
MitoProteome | Human Mitochondrial Protein Database
*** MitProNet | Mitochondrial proteome
MitoMiner | Mitochondrial proteome
*** MitoCarta2.0 | inventory of mammalian mitochondrial proteins
MPIC | mitochondrial Protein Import Components
YDPM | Proteomics of Mitochondria Databases
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
MatrisomeDB | normal and tumor extracellular matrices
COMPARTMENTS | subcellular localization database
TISSUES | tissue expression database
PredHSP | heat shock proteins and 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
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
CMPD | cancer mutant proteome database
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
PTM specific
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 mass spectrometry
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
*** PTMprober | deciphering proteome-specific PTM sites atlas
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
-----------------------------
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
DeNovoPTM | de novo sequencing with limited no. PTM occurrences per peptide
DAPPLE 2 | PTM sites using data for 19 different PTMs from 16 databases
Peiman | enrichment analysis in post translational modification (PTM) types
*** FragMixer | auto. phosphopeptide ident. using multiple MS/MS fragment. modes
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
Prospect | predict protein histidine phosphorylation sites in bacteria
-----------------------------
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
*** SSPKA | species-specific prediction of lysine acetylation
*** Succ | machine learning approach predict. species-specific succinylation sites
*** SuccFind | prediction of succinylation sites in proteins
SwissPalm | protein S-palmitoylation database
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
*** MaloPred | prediction of species-specific malonylation sites
PRmePRed | protein arginine methylation prediction tool
-----------------------------
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 and 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
*** gFinder | for the analysis of N-glycopeptides
PepSweetener | manual annotation of intact glycopeptide MS spectra
UniCarbkb | knowledge platform for glycoproteomics
GRITS | annotation of glycomics mass spectrometry 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
*** GlycoPepGrader | identifies glycopeptide candidate responsible MS spectrum
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
-----------------------------
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 and expression data
OrthoDB | hierarchical catalog of orthologs
InParanoid | ortholog groups with inparalogs
OrthoInspector | package dedicated to orthology inference and 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
-----------------------------
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
*** SysMO | systems biology of microorganisms
CodaChrome | bacterial proteome comparison with GenBank finished bacterial genomes
PVCbase | resource for the PVC bacterial proteomes
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 and proteomic data of 23 Leptospira species
*** CyanOmics | Synechococcus sp. PCC 7002 omics data
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
LoQAtE | localization and quantitation atlas of the yeast proteome
FPD | fungi phosphorylation database
Plant-PrAS | physicochemical, structural properties & novel functional regions
PPDB | Plant Proteome DataBase for A.thaliana & maize
PlantPepDB | manually curated plant peptide database
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
*** Wheat | proteome and sub-proteoms
-----------------------------
TriTrypDB | incl. MS data for Trypanosoma brucei, cruzi & leishmania
*** toxoMINE | multi omics database for T.gondii
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
Metaproteomics
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
Cobia | prediction & consequences of cofragmentation in metaproteomics
Mass Spec Tools
Skyline | MacCoss Lab Software - targeted proteomics environment
......Percolator | peptide identification from shotgun proteomics datasets
......Panorama
......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 PD nodes
......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
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
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
MSFragger | fragment-ion indexing for peptide ident. & proteomic search engine
FragPipe | GUI for running MSFragger and Philosopher
MSFragger PD-nodes | fragment-ion indexing for peptide ident. & proteomic search engine
Philosopher | complete toolkit for shotgun proteomics data analysis
PINT | store, query, & visualize large proteomic experiment results
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
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
*** SCRIPT-MAP | MS response curve of entire peptide-transition ions
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
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 and Fragment Calculator Software
MaConDa | MS Contaminants Database
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 and Analysis
RawTools | scan data parsing & quantification, QC of Thermo Orbitrap raw MS files
Informed Proteomics | algorithms for proteomic mass spectrometry 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 | mass spectrometry utility for proteomics
IPSA | interactive peptide spectral annotator
Picky | simple method designer for targeted proteomics
*** SPIRE | visualize proteins & peptides from MS data
Protalizer | automated DIA proteomics data analysis
SpecOMS | all-to-all MS spectra comparisons within minutes
*** MOPED | multi-omics profiling expression database
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, visualisation & analysis of quantitative information
pyQms | generalized, fast & accurate MS data quantification
PeptideTracker | storing of info on protein concentrations in biological tissues
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
*** ProteoRed | java MIAPI API
Peptagram | converts proteomics data into HTML5 visualisation
*** Diana | algorithm and software tools for DIA-MS data analysis
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
*** POTAMOS | simplifies MS calculations for PTM proteins
msproteomicstools | python module for MS-based proteomics
protk | proteomics toolkit - command line tools in Ruby
*** PeakLink | peptide peak linking method in LC-MS/MS using wavelet & SVM
MSstats | statistical tool for quantitative MS-based proteomics
SpliceVista | splice variant analysis in shotgun proteomics data
MALDIquant | quantitative analysis of maldi MS data
xiView | visualisation of cross-linking/MS data
xiNET | visualisation 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 mass spectrometry data
seaMass | sparse signal restoration for mass spectrometry
GIRO | groupwise image registration and normalisation
TRIC | graph-based alignment software for SRM or SWATH-MS
*** The peptide simplex | sensitive quantitative proteomics
Streaming visualisation of LC-MS raw data and 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 and 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 and Analyzer
JAMSS | a GUI Java Mass Spectrometry 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, and sharing a mass spectral library
Genoppi | integrative analysis of proteomic data & genetics
OpenSlice | web-based API for large scale MS data sharing
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
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
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
Mass spectrometry and proteomics data analysis
RforProteomics | add package to 'Using R & Bioconductor for proteomics data analysis'
psims | for writing XML documents for HUPO PSI-MS mzML and mzIdentML
mzR | parser for netCDF, mzXML, mzData and mzML and mzIdentML files
MSnbase | plotting, data manip. & processing of MS proteomics data
pRolocGUI | interactive visualisation 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
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
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.
*** sapFinder | variant peptides detection and visualization in shotgun proteomics
specL | peptide spectrum matches for use in targeted proteomics
ProtMAX | large Shotgun Proteomics Mass Spectrometry data sets
Sipros | database-searching algorithm for peptide and protein identification
JAMSS | Proteomics MS Simulation in Java
*** SILVER | Stable Isotope Labeling LC-MS data Quantitative Analysis
SIMA | Simultaneous Multiple Alignment of LC/MS Peak Lists
Specialize | ident. of peptides with complex PTM from tandem MS
ProteinDecision | protein ident. using peptide-mass fingerprinting data
SpliceDB | incorporation of RNA-seq for MS DB search
Tremolo | spectral library search
MSBayesPro | bayesian protein inference for LC-MS/MS proteomics
*** DQmodel 0.2 | improved peptide detectability prediction with protein quantity
ProteinART | protein inference solutions
ProteinInfer | combinatorial perspective of the protein inference problem
PeptideReranking | with protein-peptide correspondence & precursor peak intensity info.
SRPI | Score Regularization for Peptide Identification
NITPICK | peak identification for MS data
*** FEvER | functional information from differential quantitative proteomics datasets
Anubis | automated peptide detection & Quantification in SRM data
*** SRM QC | tool for keeping track of SRM instrument performance
SapFinder | variant peptides detection & visualization in shotgun proteomics
CHAMPS | complete homology assisted MS/MS protein sequencing
ProteoCombiner | bottom-up & top-down proteomics to improve proteoform ident.
TBnovo | de novo protein sequencing by combining top-down and bottom-up MS
protViz | R package for quality checks, viz, & analysis of proteomics MS data
hmSEEKER | identification of hmSILAC doublets in MaxQuant output data
Dart-ID | retention time alignment and peptide identification confidence updates
iq | relative protein abundances from ion quantification in DIA-MS
ncGTW | targeted realignment of LC-MS Profiles
DiaLib | generation of theoretical ion library of peptides & glycopeptides for DIA
msImpute | methods for mass spectrometry 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
FLASHDeconv | high-quality feature deconvolution for top-down proteomics
IMTBX | 2D signal extraction tools ion mobility-mass spectrometry
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 | processing of top-down high-resolution mass spectrometry 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)
Bioinformatic Solutions - PEAKS
Rapid Novor - Antibody sequencing
Visualisation Tools
DEqMS | statistical testing of differential protein expression
DynOmics | computing and visualizing biomolecular systems dynamics
DrawAlignR | across run chromatogram alignment visualization
ShinyOmics | collaborative exploration of omics-data
Omics Playground | visual analytics platform for multi-omics data
vMS-Share | NIST mass spectrometry visualization and data mining repository
Cytoscape | platform for visualizing molecular interaction networks & biological pathways
ClueGO | creates, visualizes functionally grouped network of terms/pathways
PTMOracle | Co-visualisation and co-analysis of PTM & PPI data
PathBank | pathway database for model organisms
ComPPI | compartmentalized protein-protein interaction database
Proteinarium | Multi-Sample PPI Visualization & Analysis
Instant Clue | interactive analysis & visulaisation of scientific of data
PDV | an integrated proteomics data viewer
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
Peptigram | peptidomics data visualisation
PANDA-view | multiple visualisation methods
ProteomeVis | protein properties from structure to sequence evolution across proteomes
CIG-P | circular interaction graph for proteomics
msVolcano | dynamic volcano plotting for MS data
JSparklines | visualize numbers in Java tables
ProteoViz | analysis and visualization of Phosphoproteomics data sets
pViz.js | visualization of protein sequence features
*** ProHits-viz | customizable images from protein-protein interaction data
BioJS | viewer for protein sequence featuresScop3D | visualization of sequence variation of a protein on its structure
DeepPrime2Sec | protein secondary structure prediction from primary sequences
DOSE | disease ontology semantic and 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 visualisation, exploration & analysis
BatMass | mass spectrometry data visualization
CLMSVault | protein X-linking MS data analysis & visualization
Clustergrammer | for visualizing and analyzing high-dimensional data
InterMine | integrates biological data sources, for easy query & analysis
MS-Helios | a circos wrapper to visualize multi-omic datasets
PaintOmics 3 | for pathway analysis & visualization of multi-omics data
MOFA | Multi-Omics Factor Analysis
YASARA | molecular-graphics, modeling and 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
VANTED | visualization & analysis of Networks containing Exp. Data
MALDIViz | quality checks, visualizations and 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 and net projections
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
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 and 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
ICBdocker | annotation of functional & structural features of proteomes
APPRIS | annotating principal splice isoforms
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 and 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)
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 and 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
AFree 2.0 beta | Fast ALL versus ALL Proteome Comparisons
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 and 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 and transcriptome quality assessment
PASS | a proteomics alternative splicing screening pipeline
ShettiMotif | search engine for short linear motifs / domains (SLiM)
EPD | characterising proteome dynamics in both human cells and model organisms
CABRA | cluster and annotate blast results algorithm
SignalP 5.0 | presence & location of signal peptide cleavage sites
*** TAPAS | alternative splices and protein families
Punchline | identifying & comparing Pfam protein domain differences
Surfacegenie | effective prioritization of candidate cell-type specific markers
CRAPome | contaminant repository for affinity purification
MoonDB | predicted EMF proteins and set of manually curated moonlighting proteins
*** MoonProt | database of 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 and their cleavage sites
iHPDM | in silico human proteome digestion with peptide analysis & graphical vis.
Proteasix | predict proteases involved in naturally occurring peptide generation
Mechismo | mechanistic interpretations of structural modifications
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
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
*** PIPE | protein-protein interaction prediction
*** PIPE-SITES | protein binding site prediction
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
PCIA | identification of protein complexes in protein-protein interaction networks
ECL | identification of cross-linked peptides using whole database
SLiMSuite | short linear motifs (SLiMs) in proteins as functional microdomains
MotAn | motif analyzer for Protein 3D Structures
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
*** FCP | functional coverage of the proteome
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
Spritz | proteogenomic database engine
Splicify | proteogenomic ident. of disease specific protein biomarkers from mRNA splicing
PGMiner | complete proteogenomics workflow
Proteome PheWAS browser | Pphenome-wide mendelian randomization mapping
pyGeno | python package for personalized proteogenomics
PGTools | analysis and 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 and 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 and 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
PIKE | Protein Information & Knowledge Extractor
fLPS | fast discovery of compositional biases for proteins
ProGeRF | proteome & genome repeat finder tool
OrthoDB software | compute orthologs on custom data
UniRep | deep representation learner for protein engineering informatics
*** PIA | Protein Inference Algorithms fully integrated into PRIDE
SUBAcon | max entropy justif. for Naive Bayes
MetaSPS | de novo protein sequencing
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
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
*** Speedb | fast structural protein search on PDB
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
Falcon@home | high through-put server for protein structure prediction
ProtSav | protein tertiary structure analysis and 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 | ligand binding site prediction and virtual screening
SecretP v2.0 | a new method for predicting mammalian secreted proteins
CP4P | FDR QC, control procedures and computing of adjusted p-values
ASAP | Amino-acid Sequence Annotation Predictor
SpectroGene | genome annotation using top-down mass spectrometry
PrionW | identifies proteins containing gln/asp rich prion-like domains
MBPpred | prediction of membrane lipid-Binding Proteins
PGx | mapping identified peptides onto their putative genomic coordinates
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 and 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 and proteomic data
proBAMsuite | genome-based representation & analysis of proteomics data
PPIP | identification of bioactive endogenous peptides
Pawer | protein array web explorer
arrayQualityMetrics | quality metrics report for microarray data
OOMPA | microarray and proteomics analysis library
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
PiPred | deep-learning for prediction of p-helices
IonchanPred 2.0 | prediction of ion channel and 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
Pon-Sol | effects of amino acid substitution on protein solubility
IPC | isoelectric point calculator
Proteome-pI | proteome isoelectric point database
PIP-DB | protein isoelectric point database
dbAMP | database of antimicrobial peptides and relevant proteome data
PPIP | endogenous peptides identification with RNA-seq and 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
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Additional software resources that may be worth looking at beyond those listed above can be found at |
HUPO-PSI | tools implementing mzIdentML
BioDocker | repository for bioinformatics
The Barton Group | bioinformatics software tools
SPC | seattle proteome center & transproteomic pipeline
PROWL | Rockefeller software tools
biospi Laboratory | proteomics tools
openMS | C++ library (+ python bindings) for LC/MS data management & analyses
*** Indicates those sources for which links to the source software/database is currently unavailable - the original scientific article is generally still available
