NIH Proteome Special Interest Group - Links

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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 database search and de novo algorithm for protein ID

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

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

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.

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

Rapid Communications in Mass Spectrometry

NIH Home Page

This site was originally developed by Lewis Pannell and updated on June 18, 2009 by Renee Olano. Please contact Renee Olano at olanol(at)mail.nih.gov with problems or suggestions. Thanks!