|
|||||||||
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 | |||||||||
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! |