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Software Available Elsewhere:
Databases:
Sample Sources for Proteomics
Useful Sources of Information:
Tutorials:
Groups and Organizations:
NHLBI Proteomics Centers
NHLBI Clinical Proteomics Program
Journals:
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| LINKS | |||||||||
| Software at NIH: | |||||||||
| CmpSpots ....2D gel spot pairing program in Open2Dprot project (NCI, Frederick) | |||||||||
| COGs ....phylogenetic classification of proteins (NCBI) | |||||||||
| Conserved Domain Database and Search Service (NCBI, NLM) | |||||||||
| DAVID....functional annotation tools (NIAID) | |||||||||
| DBParser ....Web based software for proteomics data analysis (LNT, NIMH) | |||||||||
| EASE ....biological interpretation of lists from microarray, proteomic, and SAGE experiments (NIAID) | |||||||||
| Entrez Gene (NCBI, NLM) | |||||||||
| Entrez protein database (NCBI, NLM) | |||||||||
| Entrez Structure (NCBI, NLM) | |||||||||
| Flicker ....Comparison of 2D Electrophoretic Gels (NCI, Frederick) | |||||||||
| Genetic Association Database (NIA, CIT) | |||||||||
| GEO....gene expression/molecular abundance repository (NCBI, NLM) | |||||||||
| GO-SCAN ....Gene Ontology (GO) annotations for a list of differentially expressed genes (CIT) | |||||||||
| HomoloGene ....automated detection of homologs (NCBI, NLM) | |||||||||
| Laboratory of Kidney and Electrolyte Metabolism Proteomics Databases (NHLBI) | |||||||||
| LECB 2D PAGE ....gel image, experiment info, and landmark data sets (NCI, Frederick) | |||||||||
| MAExplorer ....microarray data-mining program (NCI, Frederick) | |||||||||
| MassSieve ....tool for parsing ms/ms search engine results (LNT, NIMH) | |||||||||
| Merge DTA/PKL Files ....for creating a single Mascot Generic Format file (CIT) | |||||||||
| Open2Dprot ....for n-dimensional protein expression data analysis (NCI, Frederick) | |||||||||
| Open Mass Spectrometry Search Algorithm (OMSSA) (NCBI, NLM) | |||||||||
| ProtPlot ....program for virtual 2D gel from CGAP mRNA expression (NCI, Frederick) | |||||||||
| PROW ....Protein reviews on the web (NCI) | |||||||||
| RAId_DbS ....database search tool (NCBI) | |||||||||
| Seg2Dgel .....2D gel spot segmentation program in Open2Dprot project (NCI, Frederick) | |||||||||
Software Available Elsewhere: | |||||||||
| AAcompIdent ....identify a protein from its amino acid composition | |||||||||
| AACompSim ....identify proteins with similar amino acid composition | |||||||||
| Aldente ....peptide mass fingerprinting | |||||||||
| APEX Quantitative Proteomics Tool ....label-free protein quantitation using standard LC-MS/MS proteomics data | |||||||||
| BindingDB ....database of measured binding affinities | |||||||||
| BioAnalyst ....commercial software for protein/peptide deconvolution and reconstruction, de novo sequencing, and peptide mapping | |||||||||
| BioGRID ....repository for interaction datasets | |||||||||
| BioIE ....extracts informative sentences from the biomedical literature | |||||||||
| BOND ....combines sequence, interaction, and related interactome data and content | |||||||||
| CBS Prediction Servers ....prediction of glycosylation sites on proteins, etc | |||||||||
| CluSTr ....classification of proteins into groups of related proteins | |||||||||
| COLOR PROTEIN SEQUENCE....color specific amino acids in a protein sequence | |||||||||
| Compute pI/Mw ....theoretical PI and molecular weight calcuations for a protein | |||||||||
| CPAS ....proteomics data management for high-throughput LC-MS/MS experiments and clinical trials. | |||||||||
| Dasty....visualize protein sequence features | |||||||||
| Database of Interacting Proteins....experimentally determined interactions between proteins | |||||||||
| Delta Mass ....A listing of mass differences caused by modifications to aa or aa substitutions | |||||||||
| DGPI....detection/prediction of GPI cleavage site (GPI-anchor) in a protein | |||||||||
| Elucidator....commercial data management system | |||||||||
| Expasy tools ....many pieces of software for proteomics research ...a faster site | |||||||||
| FindMod ....predict post-translational modifications and find single aa substitutions in peptides | |||||||||
| FindPept ....identify peptides that result from unspecific cleavage | |||||||||
| GenomeNet....Japanese network of database and computational services | |||||||||
| GlycoFragments ....b and y ions of oligosaccharides | |||||||||
| GlycoMod ....identify glycosylated peptides from a sequence and glcosylated peptide masses | |||||||||
| Glyco-Search-MS.... database searches of complex carbohydrates | |||||||||
| GOA....Gene Ontology (GO) annotations to proteins | |||||||||
| GPI-SOM....identification of GPI-anchor signals | |||||||||
| GPMAW....General Protein/Mass Analysis | |||||||||
| IDPicker....protein assembly software | |||||||||
| iHOP....Literature search network | |||||||||
| iProClass ....software for retrieving/matching protein sequences | |||||||||
| InSilicoSpectro ....database search algorithm | |||||||||
| Inspect ....peptide sequence tags to analyse MS data | |||||||||
| IntEnz ....enzyme database | |||||||||
| JenaLib ....amino acid repository | |||||||||
| MagTran ....deconvolution program | |||||||||
| MarkerView ....commercial software for protein/peptide biomarker and metabolomics profiling applications | |||||||||
| Mascot ....protein digest and identification software | |||||||||
| MASPECTRAS ....management and analysis of proteomic LC-MS/MS data | |||||||||
| MASPIC ....intensity-based tandem mass spectrometry scoring | |||||||||
| Mass Spectrometry and Biotechnology Software Resource ....links to many software packages | |||||||||
| MassAnalyzer ....protein identification software | |||||||||
| MathDAMP ....differential analysis of metabolite profiles | |||||||||
| MedGene....biomarker discovery using literature searches | |||||||||
| MetAlign....tool for the analysis, alignment and comparison of Mass Spectrometry datasets | |||||||||
| Minimotif Miner....search for short functional motifs | |||||||||
| MitoProt....Prediction of mitochondrial targeting sequences | |||||||||
| Modiro....commercial PTM identification algorithm | |||||||||
| MolQuest.... sequence analysis and molecular biology data management | |||||||||
| MRMPilot.... commercial peptide MRM assay development software | |||||||||
| MRS.... download, store, index, and query flat-file databanks | |||||||||
| Myristoylator.... predicts N-terminal myristoylation | |||||||||
| MSBlast search at EMBL ....identify protein from several short sequences | |||||||||
| msInspect ....viewing MS data and generating peptide arrays from multiple LC-MS measurements | |||||||||
| MSQuant ....tool for quantitative proteomics | |||||||||
| MultiIdent ....identify proteins from pI, molecular weight and aa compositions | |||||||||
| MultiQuant ....commercial peptide MRM quantitation software | |||||||||
| MyriMatch ....database search algorithm | |||||||||
| NetAcet ....predicts substrates of N-acetyltransferase A | |||||||||
| NetNglyc ....predicts N-Glycosylation sites | |||||||||
| NetOglyc ....predictions of mucin type GalNAc O-glycosylation sites | |||||||||
| NetPhos ....predictions for serine, threonine and tyrosine phosphorylation sites | |||||||||
| NMT ....prediction for N-terminal N-myristoylation | |||||||||
| ParAlign ....sequence similarity searches | |||||||||
| PEAKS ....commercial de novo protein identification algorithm | |||||||||
| PepID ....protein identification by peptide clustering | |||||||||
| PepNovo ....de novo protein identification algorithm | |||||||||
| PeptideCutter ....predicts potential cleavage sites | |||||||||
| PeptIdent ....identify proteins from pI, molecular weight and peptide mass fingerprinting | |||||||||
| PeptideMass ....computes masses of peptides from an enzyme digest on a protein | |||||||||
| PeptideSearch ....database searches | |||||||||
| PETAL ....chromatographic alignment of LC-MS data | |||||||||
| Phenyx ....MS data analysis | |||||||||
| PhosphaBase ....protein phosphatase database | |||||||||
| PIKE ....protein database information extraction engine | |||||||||
| PIR ....bioinformatics resource | |||||||||
| PlasmID ....repository for plasmid clone collection and distribution | |||||||||
| Popitam ....MS/MS method designed to characterize peptides with mutations or unexpected post-translational modifications | |||||||||
| PRECIS ....automated annotation system | |||||||||
| PrePS ....prenylation prediction | |||||||||
| PRIME ....information management, tracking and analysis | |||||||||
| PRIDE ....repository for proteomics data | |||||||||
| ProMass Deconvolution ....deconvolution and reporting software | |||||||||
| ProMoST....Program to calculate accurate MWT and pI values from proteins | |||||||||
| ProteinCenter....commercial proteomic data interpretation tool | |||||||||
| ProteinLynx....commercial database search algorithm | |||||||||
| ProteinPilot ....commercial protein identification software | |||||||||
| ProteinProspector ....proteomics tools for mining sequence databases in conjunction with MS | |||||||||
| ProteoIQ ....commercial proteomic data analysis software | |||||||||
| ProtParam ....computation of various physical and chemical parameters | |||||||||
| ProSight PTM ....protein identification using Top-Down approach | |||||||||
| PROWL ....protein identification tools from Rockefeller University | |||||||||
| PSORT ....prediction of protein localization sites in cells | |||||||||
| PTS1 ....prediction of peroxisomal targeting signal 1 | |||||||||
| Qscore ....program for automated SEQUEST results validation | |||||||||
| QuickGO ....gene ontology | |||||||||
| Relibase ....searches protein-ligand databases | |||||||||
| Scaffold ....data extraction from SEQUEST and Mascot results | |||||||||
| Scansite ....search a protein and predict phosphorylation sites | |||||||||
| SCOP ....structural and evolutionary relationships between all proteins whose structure is known | |||||||||
| SEBINI ....construct biological networks | |||||||||
| SEQUEST....database search algorithm | |||||||||
| Sequit! ....MS data analysis | |||||||||
| SFLD ....enzyme structure-function database | |||||||||
| SignalP....predicts the presence and location of signal peptide cleavage sites | |||||||||
| Spectrum Mill....commercial database search algorithm | |||||||||
| SRPDB ....Signal Recognition Particle Database | |||||||||
| Sulfinator....predicts tyrosine sulfation sites | |||||||||
| SUMOplot....predicts SUMO attachment | |||||||||
| SYSTERS ....Protein Family Database | |||||||||
| TagIdent ....identify a protein by pI and molecular weight, or by sequence tag (e.g. 6 aa's in sequence) | |||||||||
| TargetP ....predicts the subcellular location | |||||||||
| TCDB ....membrane transport protein database | |||||||||
| TermiNator ....predicts N-terminal methionine excision, N-terminal acetylation, N-terminal myristoylation and S-palmitoylation | |||||||||
| TOPP ....analysis of HPLC/MS data | |||||||||
| Trans-Proteomic Pipeline (TPP) ....suite of tools for the analysis of LC/MS/MS data | |||||||||
| Unimod....protein modifications database | |||||||||
| UniProt....central repository of protein sequence and function | |||||||||
| VEMS....MS data analysis | |||||||||
| WebGene....prediction of protein coding sequence | |||||||||
| X! Tandem....open source database search algorithm | |||||||||
| XplorMed....explore a set of abstracts derived from a MEDLINE search | |||||||||
| YassDB....build a database | |||||||||
| YinOYang....predictions for O-�-GlcNAc attachment sites | |||||||||
Databases: | |||||||||
| Acute Toxicity Database....aquatic acute toxicity tests | |||||||||
| Albinism Database | |||||||||
| Bodymap....expression of human and mouse genes | |||||||||
| CADRE....Aspergillus repository | |||||||||
| EXTOXNET....Pesticide Information Profiles | |||||||||
| GPCRDB ....G protein-coupled receptors | |||||||||
| GPCRIPDB ....GPCR interacting proteins | |||||||||
| The human gene mutation database | |||||||||
| Human Mitochondrial Protein Database | |||||||||
| Human Myocardial Two-Dimensional Electrophoresis Protein Database | |||||||||
| Human Protein Reference Database | |||||||||
| Human Red Blood Cell Database | |||||||||
| human type I and type III collagen mutations | |||||||||
| Human Unidentified Gene-Encoded Large Proteins (HUGE)....large human proteins | |||||||||
| Interactive Images of Disease....image database | |||||||||
| KChannelDB ....for Potassium channels | |||||||||
| Kidney Development Database | |||||||||
| MAPU....several body fluid proteomes | |||||||||
| Medline (Pubmed) ....literature searching | |||||||||
| MEROPS ....peptidases | |||||||||
| MHCPEP ....MHC binding peptides | |||||||||
| MINT database ....protein interactions | |||||||||
| MIPS Mammalian Protein-Protein Interaction Database | |||||||||
| MitoDat ....human nuclear-encoded mitochondrial proteins | |||||||||
| MitoProteome ....mitochondrial protein sequence database | |||||||||
| NDB ....three-dimensional structural information about nucleic acids | |||||||||
| NIST Chemistry WebBook ....thermochemical, thermophysical, and ion energetics data | |||||||||
| NucleaRDB ....Nuclear Receptors | |||||||||
| Nucleic acid � Protein Interaction Database | |||||||||
| O-GlycBase....database of O- and C-glycosylated proteins | |||||||||
| Obesity Gene Map Database | |||||||||
| Pathema | |||||||||
| Pedant genome database | |||||||||
| Peptaibol Database | |||||||||
| PeptideAtlas Builds | |||||||||
| PeptideAtlas repository....raw LC/MS/MS files | |||||||||
| Pfam ....multiple sequence alignments | |||||||||
| Phospho.ELM ....experimentally verified Serine, Threonine and Tyrosine phosphorylation sites | |||||||||
| Phosphorylation Site Database | |||||||||
| PRINTS ....protein fingerprints | |||||||||
| PrionDB ....Prion proteins | |||||||||
| ProDom ....protein domain families | |||||||||
| Protein-Protein Interactions Table for Human herpesvirus 1 | |||||||||
| Retrovirus Tagged Cancer Gene Database (RTCGD) | |||||||||
| Secreted Protein Database | |||||||||
| TIGR's Genome Projects | |||||||||
| TOXNET....toxicology, hazardous chemicals, environmental health, and toxic releases | |||||||||
| Universal Mutation Database (UMD)....mutations associated with genetic diseases | |||||||||
| USPTO....US patent search | |||||||||
Sample Sources for Proteomics | |||||||||
| NCI Office of Biorepositoriers and Biospecimen Research | |||||||||
| NCI Specimen Resource Locator | |||||||||
| Alzheimer Research Forum list of Brain Banks | |||||||||
| Asterand | |||||||||
| Bioreclamation | |||||||||
| Capital Biosciences | |||||||||
| Cooperative Human Tissue Network (CHTN) | |||||||||
| Human Brain and Spinal Fluid Resource Center | |||||||||
| Integrated Laboratory Services - Biotech (ILSbio) | |||||||||
| MatTek Corporation | |||||||||
| National Disease Research Interchange | |||||||||
| National Pathology Repository | |||||||||
| PathServe Autopsy And Human Tissue Bank | |||||||||
| Pel-Freez Biologicals | |||||||||
| SeraCare BioProcessing | |||||||||
Useful Sources of Information: | |||||||||
| National Library of Medicine | |||||||||
| PROLYSIS ....a protease and protease inhibitor Web server | |||||||||
| Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank....an Information Portal to Biological Macromolecular Structures | |||||||||
| The human protein atlas ....high resolution images of immunohistochemically stained tissues and cell lines | |||||||||
| Human Disease Glycomics/ Proteome Initiative (HGPI) | |||||||||
| The Nature/CFG Glycomics Gateway | |||||||||
| Glycosciences....tools for glycobiology | |||||||||
| The Plasma Proteome Institute | |||||||||
| spectroscopyNOW....resource for the spectroscopy community | |||||||||
| MSLinks.com ....Extensive listing of mass spectrometry resources | |||||||||
| proteomicsSURF....disease proteomics and proteomic technologies | |||||||||
| Bioinfo Online ...source for bioinformatics related information | |||||||||
| Mass Spectrometry Blog ...Web Log of Mass Spectrometry Web Sites and Other Links and Items of Interest | |||||||||
| ProteomeCommons.org ...proteomics website | |||||||||
| The Biomarkers Consortium | |||||||||
| IFTI-MIRAGE website | |||||||||
| Neal's DNA Mutation Site | |||||||||
| Database of Macromolecular Movements | |||||||||
| Impact factor of Journals | |||||||||
| Defense Advanced Research Projects Agency | |||||||||
| National Center for Health Statistics | |||||||||
| Biocarta Pathways | |||||||||
| Metabolomics.net....metabolic portal | |||||||||
| Profiles in Science....twentieth-century leaders in biomedical research and public health | |||||||||
| Nobelprize.org....Nobel Prize Information | |||||||||
| National Center for Research Resources....Proteomics software and Tools | |||||||||
Tutorials: | |||||||||
| A History of Mass Spectrometry...by Scripps Center for Mass Spectrometry | |||||||||
| An Introduction to Mass Spectrometry ...by Alison E. Ashcroft | |||||||||
| Introduction to Mass Spectrometry ...by Ludwig Gruber | |||||||||
| I-mass link site for tutorials | |||||||||
| MSeminar: Mass Spectrometry Webinars ....by Thermo Fisher Scientific | |||||||||
| Pioneers of Proteomics | |||||||||
| Proteomic Technologies and Cancer | |||||||||
| 2-Dimensional Ion Trap ....tutorial by Thermo Fisher Scientific, Inc | |||||||||
| Ion Trap Mass Spectrometry ....tutorial by IonSource | |||||||||
| Interpreting Electrospray Mass Spectra ....tutorial by IonSource | |||||||||
| Principles of MS Quantitation ....tutorial by IonSource | |||||||||
| The Whys and Wherefores of Quadrupole Ion Trap Mass Spectrometry ....by Karen R. Jonscher and John R. Yates, III | |||||||||
| Time of Flight Mass Spectrometry ....tutorial by Jordan TOF Products, Inc. | |||||||||
| Laser tutorial | |||||||||
| Setting Up Two-Dimensional Gel Electrophoresis for Proteome Projects | |||||||||
| Stuctural Analysis of Proteins and Peptides in the Presence of Detergents: Tricks of the Trade | |||||||||
| Analytical Chemistry I and II....by James K. Hardy | |||||||||
| High Performance Liquid Chromatography | |||||||||
| Chrom-Ed Series | |||||||||
| HPLC for Pharmaceutical Scientists | |||||||||
| On-Line HPLC Course | |||||||||
| HPLC Column Companion ....by MAC-MOD Analytical, Inc. | |||||||||
| EARL....analytical reference library | |||||||||
| Thomas Chasteen's movies ....electrophoresis, spectroscopy, chromatography, chemiluminescence, etc. | |||||||||
| Capillary Electrophoresis ....by Yan Xu | |||||||||
| Capillary Electrophoresis website ....by Tony Dixon | |||||||||
| PubMed Tutorial | |||||||||
| Gene and Protein Database Guide | |||||||||
| Mass Spectrometry of Fatty Acid Derivatives | |||||||||
| Principles of Clinical Pharmacology | |||||||||
| NIH Funding Opportunities, Peer Review and Grant Writing | |||||||||
| Demystifying Medicine | |||||||||
Groups and Organizations: | |||||||||
| NIH Mass Spectrometry Interest Group | |||||||||
| Mass Spectrometry Interest Group of the NCI at Frederick | |||||||||
| NIH Structural Biology Interest Group | |||||||||
| NIH Glyco Interest Group | |||||||||
| NIH Translational Research Interest Group | |||||||||
| NIH Immunology Interest Group | |||||||||
| Greater Washington-Baltimore area Mass Spectrometry Discussion Group | |||||||||
| American Society for Mass Spectrometry | |||||||||
| Human Proteome Organisation | |||||||||
| Association of Biomolecular Resource Facility: includes MS features and links | |||||||||
| The Proteome Society | |||||||||
| Montreal Proteomics Network | |||||||||
| International Mass Spectrometry Foundation (IMSF) | |||||||||
| HUPO Proteomics Standards Initiative | |||||||||
| Swiss Proteomics Society | |||||||||
NHLBI Proteomics Centers | |||||||||
| Boston University Cardiovascular Proteomics Center | |||||||||
| Johns Hopkins Proteomics Center | |||||||||
| Medical College of Wisconsin Proteomics Center | |||||||||
| Medical University of South Carolina Proteomics Center | |||||||||
| Seattle Proteome Center | |||||||||
| Stanford University Proteomics Center | |||||||||
| Uniformed Services University Cystic Fibrosis Proteomics Center | |||||||||
| University of Texas Medical Branch at Galveston | |||||||||
| University of Texas Southwestern Medical Center in Dallas | |||||||||
| Yale Proteomics Center | |||||||||
NHLBI Clinical Proteomics Program | |||||||||
Journals: | |||||||||
| Clinical Proteomics | |||||||||
| Electrophoresis | |||||||||
| Journal of the American Society for Mass Spectrometry | |||||||||
| Journal of Chromatography B: Biomedical Sciences and Applications | |||||||||
| Journal of Mass Spectrometry | |||||||||
| Journal of Proteome Research | |||||||||
| Mass Spectrometry Reviews | |||||||||
| Molecular and Cellular Proteomics | |||||||||
| Nature Biotechnology | |||||||||
| Protein Science | |||||||||
| Proteomics | |||||||||
| Rapid Communications in Mass Spectrometry | |||||||||
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| This site was originally developed by Lewis Pannell and updated on December 16, 2008 by Renee Olano. Please contact Renee Olano at olanol(at)mail.nih.gov with problems or suggestions. Thanks! |