NIH Proteomics Interest Group
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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
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 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 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 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 database search and de novo algorithm for protein ID
PepID ....protein identification by peptide clustering
PepNovo 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 extraction from SEQUEST and Mascot results
Scansite 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! source database search algorithm
XplorMed....explore a set of abstracts derived from a MEDLINE search a database
YinOYang....predictions for O--GlcNAc attachment sites

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
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
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
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 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 for glycobiology
The Plasma Proteome Institute
spectroscopyNOW....resource for the spectroscopy community ....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 ...proteomics website
The Biomarkers Consortium
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
Profiles in Science....twentieth-century leaders in biomedical research and public health Prize Information
National Center for Research Resources....Proteomics software and Tools

A History of Mass Scripps Center for Mass Spectrometry
An Introduction to Mass Spectrometry Alison E. Ashcroft
Introduction to Mass Spectrometry Ludwig Gruber
I-mass link site for tutorials
MSeminar: Mass Spectrometry Webinars 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 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 James K. Hardy
High Performance Liquid Chromatography
Chrom-Ed Series
HPLC for Pharmaceutical Scientists
On-Line HPLC Course
HPLC Column Companion MAC-MOD Analytical, Inc.
EARL....analytical reference library
Thomas Chasteen's movies ....electrophoresis, spectroscopy, chromatography, chemiluminescence, etc.
Capillary Electrophoresis Yan Xu
Capillary Electrophoresis website 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

Clinical Proteomics
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
Rapid Communications in Mass Spectrometry

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This site was originally developed by Lewis Pannell and updated on August 6, 2013 by Renee Olano. Please contact Renee Olano at olanol(at) with problems. Thanks!