PEP Talk January 7-11, 2008 • Coronado, California

Applications  Map: Finding guide to terms in these glossaries  Site Map
Related glossaries include Proteomics categories 
Applications: Functional genomics,  Metabolic engineering, Structural Genomics  
Informatics Algorithms,  In silico & Molecular Modeling,   Information Management & Interpretation
Technologies:  Chromatography & electrophoresis,  Mass spectrometry,  Microarrays & protein chips,  NMR & x-ray crystallography
Biology: Expression,  Proteins,  Protein Structure 

2D gel electrophoresis: A key technology for proteomics. Chromatography & electrophoresis glossary

allosteric ribozymes (allozymes): Pharmaceutical biology glossary Potential for use in proteomics.

annotation- proteins: The annotation of a protein sequence needs the following steps: protein classification into defined groups according to its homology to well characterized proteins, relevant literature is given by a link to Pub- Med, protein assignment into at least one functional category.  Complete genome annotation, Munich Information Center for Protein Sequences MIPS, 2003 http://mips.gsf.de/projects/annotation

In SWISS- PROT, as in most other sequence databases, two classes of data can be distinguished: the core data and the annotation. For each sequence entry the core data consists of the sequence data, the citation information (bibliographical references), and the taxonomic data (description of the biological source of the protein), while the annotation consists of the description of the following items: Function(s) of the protein, Post- translational modification(s). For example carbohydrates, phosphorylation, acetylation, GPI- anchor, etc., Domains and sites. For example calcium binding regions, ATP- binding sites, zinc fingers, homeobox, kringle, etc., Secondary structure, Quaternary structure, Similarities to other proteins, Disease(s) associated with deficiencie(s) in the protein, Sequence conflicts, variants, etc. [Rolf Apweiler et. al " Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS- PROT + TrEMBL" Intelligent Systems in Molecular Biology, 1997]  http://www.ebi.ac.uk/swissprot/Publications/ismb97.html

Narrower terms: annotation- proteomes, functional annotation - proteome

antibody arrays: Microarrays & protein chips categories for studying regulation at the protein level

bait: The basic format of the yeast-two hybrid system involves the creation of two hybrid molecules, one in which the "bait" protein is fused with a transcription factor, and one in which the "prey" protein is fused with a related transcription factor. If the bait and prey proteins indeed interact then the two factors fused to these two proteins are also brought into proximity with each other. As a result a specific signal is produced, indicating an interaction has taken place.

binary interactions: It is important to realize that there is not a single, clear definition of a 'binary interaction'. In case of the MIPS protein complexes, the matrix representation, in which each complex is represented by the set of binary interactions corresponding to all pairs of proteins from the complex, is almost exclusively. used. For complex pull-down experiments, two different representations have been proposed: the matrix representation and the spoke representation in which only bait- prey interactions are included. Lars J. Jensen, Peer Bork, Quality analysis and integration of large- scale molecular data sets. Drug Discovery Today: Targets, 3(2): 51-56.

biological atlas: Maps, genomic & genetic glossary

cell expression profiles: Cell biology glossary

cell mapping: Maps genomic & genetic Can determine subcellular locations of proteins.

cellular pathways: Metabolic engineering See under  metabolic engineering

cellular proteome: All of the proteins expressed in a cell.

Google = about 948 Oct. 25, 2006

chemoproteomics: -Omes & -omics glossary

Google = about 503 Oct. 25, 2006

clinical proteomics: Molecular Medicine glossary

Google = about 435 Sept. 18, 2002; about 96,900 Oct. 25, 2006

combinatorial peptide libraries: Combinatorial libraries & synthesis

complete proteome sets: We consider as "complete" genomes that have been fully closed and for which there are good gene prediction models. ... For bacterial and archaeal genomes, whole-genome shotguns (WGS) and draft sequences are not included in the UniProtKB complete proteome sets and are not considered for manual annotation. ...For eukaryotic genomes, several criteria apply to consider a proteome "complete". Some sequenced genomes have submission/annotation problems that prevent the production of a non-redundant protein set; others have problems regarding the gene model predictions. UniProt, What are complete proteome sets? 2007 http://beta.uniprot.org/faq/15 

DNA protein interactions: See protein- DNA interactions

degradomics: -Omes & -omics glossary

Google = about  59 Sept. 18, 2002' about 641 Oct. 25, 2006

designer proteins: Protein categories

Google = about  314 Sept. 18, 2002, about 10,900 Oct. 25, 2006

differential labeling: Labeling, signaling & detection glossary Used for comparing the proteomes of different cell states. 

directed protein evolution: http://cat.inist.fr/?aModele=afficheN&cpsidt=17092756 

Google = about 902 Oct. 25, 2006

dissociator assays: A collective term for yeast- one hybrid, yeast- two hybrid or yeast- three hybrid assays.

Google = about 25 Oct. 25, 2006

domain: Protein structure glossary

evolutionary genomics, evolutionary homology:  Phylogenomics glossary

Expressed Protein Tags EPTs: Represent the collection of proteins which are present in a cell. [Robert G. Urban "Proteomics: Making sense of the census" Current Drug Discovery, Aug. 2001]  http://www.current-drugs.com/CDD/CDD/CDDContents-August.htm

Related term: DNA glossary EST expressed sequence tags 

FlexGene repository:  FLEX Full- Length Expression http://www.hip.harvard.edu/flex_gene/index.htm 

fragmentome:  -Omes & -omics glossary

functional protein microarrays: Microarrays categories

functional proteomics: Proteomics categories

Google = about 3,160 Sept. 18, 2002; about 152,000 Oct. 25, 2006

glycosylation: Proteins glossary

guilt by association: Expression glossary

HUPO: SEE Human Proteome Project

Hidden Markov Models HMM: In silico & Molecular modeling glossary

high-density protein arrays: Microarrays categories 

high- throughput proteomics: Proteomics categories 

homointeraction: A lot of proteins interact with themselves. [Dr. Jong Paik, Bioinformatics/ Proteomics, Dunn Human Nutrition Unit, Medical Research Council,  UK, 2001] http://www.mrc-dunn.cam.ac.uk/research/bioinformatics_proteomics.html

homolog, homologue, homology: Functional Genomics

homology modelling: Structural genomics glossary

Human Plasma Proteome: See under Human Proteome

Human Proteome: See Plasma Proteome  

Human Proteome Organisation HUPO: The reason for creating HUPO is to assist in increasing the awareness of this discipline of science across society, particularly with regard to the Human Proteome Project and to engender a broader understanding of the importance of proteomics and the opportunities it offers in the diagnosis, prognosis and therapy of disease. As a global body it will also have the objective of fostering international cooperation across the proteomics community and of promoting scientific research in an on- going manner around the world.. HUPO Human Proteome Organisation website: http://www.hupo.org/

Human Proteomics Initiative: http://au.expasy.org/sprot/hpi/  Swiss Institute of Bioinformatics'  major project to annotate all known human sequences according to the quality standards of SWISS- PROT. This means providing, for each known protein, a wealth of information that include the description of its function, its domain structure, subcellular location, post- translational modifications, variants, similarities to other proteins, etc. 

immunoproteomics: -Omes & -Omics glossary

interaction proteomics: Proteomics categories

Google = about  73 Sept. 18, 2002; about 403 Feb. 17, 2005; about 697 Oct. 25, 2006

interactome, interactomics: Omes & omics glossary

interologs: Protein interaction maps have provided insight into the relationships among the predicted proteins of model organisms for which a genome sequence is available. These maps have been useful in generating potential interaction networks, which have confirmed the existence of known complexes and pathways and have suggested the existence of new complexes and or crosstalk between previously unlinked pathways. However, the generation of such maps is costly and labor intensive. Here, we investigate the extent to which a protein interaction map generated in one species can be used to predict interactions in another species. [LR Matthews "Identification of potential interaction networks using sequence- based searches for conserved protein- protein interactions or "Interologs" Genome Research 11 (12): 2120- 2126, Dec. 2001]

Isotope Coded Infinity Tag ICAT:  These tags provide the ability to both identify and quantify a broad range of proteins in a high- throughput mode. Using ICAT reagents, researchers can compare the expression levels of proteins from two samples, such as from normal and diseased cells. ICAT reagents comprise a protein reactive group, an affinity tag (biotin), and an isotopically labeled linker. 

Related term: protein profiling

localization: SEE protein localization: Proteins glossary

localizome: Omes & omics glossary

localizome mapping: Maps, genomic & genetic glossary

microfluidics: Nanoscience & Miniaturization glossary

MudPIT Multidimensional Protein identification Technology:  

Related term: Databases & Software Directory SEQUEST [software]

NHLBI Proteomics Initiative:

ORFeome: Omes & omics glossary

ontologies - proteomics: A principal aim of post- genomic biology is elucidating the structures, functions and biochemical properties of all gene products in a genome. However, to adequately comprehend such a large amount of information we need new descriptions of proteins that scale to the genomic level. In short, we need a unified ontology for proteomics. Much progress has been made towards this end, including a variety of approaches to systematic structural and functional classification and initial work towards developing standardized, unified descriptions for protein properties. In relation to function, there is a particularly great diversity of approaches, involving placing a protein in structured hierarchies or more- generalized networks and a recent approach based on circumscribing a protein's function through systematic enumeration of molecular interactions. N Lan, GT Montelione, M. Gerstein, Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level, Current Opinion in Chemical Biology 7(1): 44- 54, Feb. 2003

Peptalk: The Protein Information Week January 7 - 11, 2008 • San Diego CA  

peptide mapping, peptide maps: Maps, genomic & genetic

peptidomics: -Omes & -omics glossary

Google = about  180 Sept. 18, 2002; about 748 July 14, 2004

perturbagens: Peptides or protein fragments that, when expressed in cells, create desirable shifts in phenotype. These phenotypic probes ("perturbagens") can be used in turn to define their binding partners using a variant of yeast two- hybrid methodology. Drs. Jon Karpilow, Giordano Caponigro,  Arcaris Inc. "Trans- FACS Analysis in Melanoma" CHI Gene Functional Analysis, Mar. 2-3, 2000, San Francisco CA 

Used in physics to determine the effects of a number of variables upon a system.

phage display: Genetic manipulation & disruption 

phage display peptide libraries: Combinatorial libraries & synthesis

pharmacoproteomics:   Pharmacogenomics

Google = about 195 Sept. 18, 2002, about 488 July 14, 2004; about 12,200 Oct. 25, 2006

phosphoproteome, phosphoproteomics : Proteomics categories glossary

phosphorylation: Proteins glossary

phylogenetic profiles: Phylogenomics glossary Can be used to hypothesize protein function.

plasma proteome: Comprehensive, systematic characterization of the plasma proteome in healthy and diseased states greatly facilitates the development of biosignatures for early disease detection, clinical diagnosis, and therapy. However, blood plasma is the most complex human-derived proteome containing other tissue proteome subsets as well as a wide dynamic range of protein concentrations.  Mining the Plasma Proteome: Discovering Biomarkers for Diagnostics/Prognostics and Drug Discovery/ Development, January 7-9, 2008, San Diego, CA

post-proteomics:  Companies are taking position at the end stages of drug discovery in the hopes that industry- wide efforts in gene expression, protein expression, protein- protein interaction and other proteomic studies will yield many disease targets that must have their function verified. But to become a marketable solution for the industry, they must significantly increase the scale of functional experiments such as animal models and cell assays that, historically, have not been easily scaled. "The Current State of Proteomic Technology" CHI's GenomeLink 3.1 http://www.healthtech.com/newsarticles/issue3_1.ASP

post- translational modification identification: ExPASy Proteomics Tools http://www.expasy.ch/tools/#ptm  list a number of tools for prediction of post- translational modification, as do other websites. Identification of these modifications may provide important structural- functional information.

post-translational modifications: Proteins glossary

prey: See under yeast two hybrid 

protein: Proteins glossary

protein analysis: http://www.indianacaps.com/index.php?option=com_content&task=view&id=24&Itemid=43 

protein and mRNA data: Although the relationship between  mRNA and protein levels is vague for individual genes, some of the statistics for broad categories of protein properties are much more robust... In contrast to the differences between mRNA and protein data for individual genes, the broad categories show that the transcriptome and translatome populations are remarkably similar; both contain roughly the same proportions of secondary structure and functional categories. Moreover, this contrasts the difference with the genome, which appears to have a distinctly different composition of functional categories. This illustrates that we get a more consistent picture when we average across the population, i.e. there is broad similarity between the characteristics of highly expressed mRNA and highly abundant proteins.  Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of  Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001 http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf  

Related terms: Expression glossary; Genomics glossary genome data; functional genomics data Omes & omics transcriptome, translatome

protein annotation - dictionary-driven For many years, computational methods seeking to automatically determine the properties (functional, structural, physiochemical, etc.) of a protein directly from sequence have been the focus of numerous research groups, including ours. By general admission, this is a difficult problem and the methods that have been proposed over the years typically concentrated on the analysis of individual genes. With the advent of advanced sequencing methods and systems, the number of amino acid sequences and fragments being deposited in the public databases has been increasing steadily. This in turn generated a renewed demand for automated approaches that can quickly, exhaustively and objectively annotate individual sequences as well as complete genomes. In this paper, we present one such approach. The approach is centered around and exploits the Bio- Dictionary, an exhaustive collection of amino acid patterns (referred to as seqlets) that completely covers the natural sequence space of proteins to the extent that this space is sampled by the currently available public databases. Isidore Rigoutsos, Tien Huynh, Laxmi P. Parida, Daniel E. Platt, Aris Floratos, Dictionary Driven Protein Annotation, Nucleic Acids Research, 30 (no 17) 3901- 3916, 2002 

protein arrays: Microarrays & protein chips glossary

Google = about  2,050 Sept. 18, 2002; about 10,200 July 14, 2004; about 194,000 June 11, 2007

protein biomarkers: Biomarkers glossary

protein capture/proteome tools:  The Proteome is the complete set of proteins in the body. Efforts in this area would support developing and making available to the scientific community high quality probes specific to every protein in the human and in desired animal models. This would allow the ability to characterize protein function in health and disease and to monitor the markers of a disease in order to deploy early prevention efforts and to identify potential therapeutic targets. New Roadmap Emphasis areas for 2008, NIH Roadmap, http://nihroadmap.nih.gov/2008initiatives.asp 

protein- carbohydrate interactions: The overarching goal of the [Consortium for Functional Glycomics] program is to: Define paradigms by which protein-carbohydrate interactions mediate cell communication. Consortium for Functional Glycomics, funded by NIGMS, US  http://web.mit.edu/glycomics/consortium/organization/program/program.shtml

protein chips: Microarrays & protein chips glossary

Google = about  2,450 Sept. 18, 2002; about 7.450 July 14, 2004; about 113,000 Nov 10, 2006 

protein complexes:   http://en.wikipedia.org/wiki/Protein_complex 

Google = about  23,900 Sept. 18, 2002; about 151,000 July 14, 2004; about 806,000 Nov 10, 2006

Related terms: complexome: -Omes & -omics glossary; Metabolic engineering glossary

protein-DNA interactions: Can be detected by DNA footprinting, gel shift analysis, yeast one hybrid assays or Southwestern blots. John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College  http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html 

Can also be analyzed by genetic analysis and X-ray crystallography. [John Little Biochemistry Fall 2000, University of Arizona]

Related terms: Proteomics categories  interaction proteomics

protein databases: Protein location can be determined by such genome- wide techniques as green fluorescent protein (GFP) tagging, and protein- protein interactions can be determined by affinity chromatography, immunoprecipitation and yeast two- hybrid experiments. Databases resulting from these methods are beginning to emerge, but they are of uncertain accuracy. Defining the Mandate of Proteomics in the Post- Genomics Era, Board on International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html

Dr. Stanley Fields, Professor of  Genetics and Medicine at the Univ. of Washington and developer of the yeast two hybrid system writes that protein databases "will need to become much more sophisticated if they are to help scientists make sense of the staggering number of experimental measurements that will soon emerge. ...  protein data will need to be integrated with results from expression profiling, genome- wide mutation or antisense analyses, and polymorphism detection. As proteomic data accumulate, we will become better at triangulating from multiple disparate bits of information to gain a bearing on what a protein does in the cell. S. Fields "Proteomics in Genomeland" Science 291: 1221-1224 Feb. 16, 2001

Related terms: protein identification, protein localization; Expression glossary expression profiling

Protein databases Databases & software directory

protein dynamics: Certain parts of a particular protein will be rigid, but others may be flexible and change their shape, even when bound. ... NMR has the unique ability to characterize protein fluctuations quantitatively, much more so than crystallography can. 

Understanding the function of a protein is fundamental for gaining insight into many biological processes. Proteins are stable mechanical constructs that allow certain internal motions to enable their biological function. Structural properties of a protein can be obtained with X-ray crystallography or NMR acquisition techniques. Molecular dynamics (MD) simulations at pico/ nano- second time scales output one or more trajectory files which describe the coordinates of each individual atom over time. The main problem with animating these trajectories is one of  temporal scale. Taking large time steps will destroy the impression of smooth motion, while small time steps will result in the camouflage of interesting motions. [Henk Huitema, Robert van Liere " Interactive Visualization of Protein Dynamics" ERCIM [European Research Consortium for Computers and Informatics] News No. 44 - January 2001]  http://www.ercim.org/publication/Ercim_News/enw44/van_liere.html

Google = about  5,800 Sept. 18, 2002; about 18,200 July 14, 2004; about 295,000 Nov 10, 2006

protein expression: Is variable, not all encoded proteins are expressed at all times. More ... Expression glossary

Google = about 68,000 Sept. 18, 2002; about 544,000 July 14, 2004; about 1,410,000 Nov 10, 2006

protein expression mapping: Maps, genetic & genomic glossary

protein expression profiling: Expression glossary

protein folding disorders: Molecular medicine glossary

protein function: Function is not a fixed property for many, if not most proteins. There are many ways that gene products can be altered to elicit modified or completely new functions. For example there are exist - alternative splicing - which may affect as many as ¼ or more of the genes in a higher eukaryote and can alter biochemical function either drastically or subtly, producing truncated proteins and proteins with different compositions - post- translational modification, such as phosphorylation and glycosidation (which can occur on numerous sites on the same protein) - pre-enzymes made for secretion and pro- enzymes that are activated by cleavage - acylation and ubiquitination - non- enzymatic modifications like oxidation, so a given protein exists in the cell in different oxidized states. Defining the Mandate of Proteomics in the Post- Genomics Era, Board on International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html

More systematic attempts have been made to place proteins within a hierarchy of standard functional categories or to connect them in overlapping networks of varying types of associations.  These networks can obviously include protein- protein interactions ... More broadly, they can include pathways, regulatory systems and signaling cascades... Perhaps, in the future, the systematic combination of networks may provide for a truly rigorous definition of protein function. Mark Gerstein, et. al "Integrating Interactomes" Science 295 (5553): 284, Jan. 2002   

A biologically useful definition of the function of a protein requires a description at several different levels. To the biochemist, function means the biochemical role of an individual protein: if it is an enzyme, function refers to the reaction catalyzed; if it is a signaling protein, function refers to the interactions that the protein makes. To the geneticist or cell biologist, function includes these roles but will also encompass the cellular roles of the protein, such as the phenotype of its deletion, the pathway in which it operates, among others. A physiologist or developmental biologist may have an even broader view of function, including tissue specificity and expression during the life cycle of the organism. Gregory A Petsko, Dagmar Ringe "Overview: The Structural Basis of Protein Function" from Chapter 2 of Protein Structure and Function: New Science Press, 1991-2001 http://www.biomedcentral.com/nspprimers/proteinfunction/full  [subscription required for access]

In the expanded view of protein function, a protein is defined as an element in the network of its interactions. Various terms have been coined for this expanded notion of function, such as ‘contextual function’ or ‘cellular function’ … Whatever the term, the idea is that each protein in living matter functions as part of an extended web of interacting molecules … Often it is possible to understand the cellular functions of uncharacterized proteins through their linkages to characterized proteins. In broader terms, the networks of linkages offer a new view of the meaning of protein function, and in time should offer a deepened understanding of the function of cells. [David Eisenberg et al "Protein function in the post- genomic era" Nature 405: 823- 826, 15 June 2000]

The principal problem facing the post- genome era. [Walter Blackstock & Malcolm Weir "Proteomics" Trends in Biotechnology: 121-134 Mar 1999]

Google = about 27,400 Sept. 18, 2002 about 58,400 Aug. 18, 2003, about 133,000 July 14, 2004; about 766,000 Nov 10, 2006

Related terms: Protein categories interaction proteomics; Functional genomics glossary gene function, Gene Ontology^TM ; Maps  cell mapping

protein identification: The analytical method used most commonly to visualize and identify large numbers of proteins is 2D-gel electrophoresis. One can theoretically visualize changes in protein production, both qualitatively and quantitatively, from two individual samples (e.g., a control preparation and a treated preparation). Furthermore, one can potentially accomplish protein identification by "picking" proteins from the 2D- gel and subjecting the highly purified protein to MALDI- TOF mass spectrometry.  "High - Throughput Genomics, CHI Genome Link 14.1 http://www.healthtech.com/newsarticles/issue14_1.asp

Google = about  8,460 Sept. 18, 2002 about 15,000 Aug. 18, 2003, about 32,000 July 14, 2004; about 494,000 Nov 10, 2006

Related term: protein databases

protein informatics: The Protein Informatics Group currently consists of a collaboration between researchers at the Oak Ridge National Laboratory, the University of Missouri, and the University of Georgia. Our common interests are in development of computational tools for solving problems from molecular biology. Our work ranges from construction of mathematical/statistical models to development of algorithms to code implementation on various platforms to applications of computational tools to solve various bio-data analysis problems.  Protein Informatics Group, Computational Biology, Oak Ridge National Lab, US http://compbio.ornl.gov/structure/ 

Although mining of protein structure homology data is a relatively small field now, it is likely to experience dramatic growth and to become pivotal in the ultimate exploitation of genomic data and tools. [CHI Target Validation report]

Google = about 561 Sept. 18, 2002, about 888 Aug. 18, 2003, about 1,810 July 14, 2004; about 16,200 Nov 10, 2006

Related terms: proteoinformatics; Algorithms glossary;  Bioinformatics glossary protein bioinformatics; In Silico & molecular modeling glossary, Structural genomics glossary

protein interactions: See protein DNA interactions, protein protein interactions, protein RNA interactions

Google = about  59,900 Sept. 18, 2002; about 141,000 Aug. 18, 2003, about 271,000 July 14, 2004; about 1.170,000 Nov 10, 2006

Narrower terms: annotation- proteins, binary interaction, interaction proteomics, protein- DNA interactions, protein- protein interactions, protein- RNA interactions; Related terms: protein networks; -Omes & -omics glossary interactome

protein interaction mapping: Maps genomic & genetic 

protein knockouts: Genetic manipulation & disruption 

Google = about 63, July 14, 2004; about 179 Nov 10, 2006

protein linkage maps: Maps genomic & genetic  

protein localization: Proteins glossary

protein microarrays: Microarrays & protein chips glossary

Google = about  1,410 Sept. 18, 2002; about 4,380 Aug. 18, 2003' about 11,000 July 14, 2004; about 198,000 Nov 10, 2006

protein networks: The individual steps in signal transduction pathways involve protein interactions with target molecules that may be other proteins, small molecules or DNA. Identifying all of the proteins that take part in a given class of interactions, on a genome-wide scale, remains an extremely challenging task. We propose to apply mRNA display (1, 2) technology to this problem, with the goal of developing databases of protein-ligand interactions that will add value to the existing and growing sequence databases. PI Jack Szostak, Definition of Protein Networks using mRNA display,  ParaBioSYs, MGH, HMS, BU     http://pga.mgh.harvard.edu/Parabiosys/projects/protein_networks_rna_display.php 

Google = about  1,160 Sept. 18, 2002; about 2,530 Aug. 18, 2003; about 6,170 July 14, 2004; about 138,000 Nov 10, 2006

Related term: protein interactions

protein profiling: Expression glossary

Google = about 1,290 Sept. 18, 2002; about 2,820 Aug. 18, 2003, about 6,700 July 14, 2004; about 192,000 Nov 10, 2006

protein- protein interactions: Protein-protein interactions (PPI) play a key role in many biological processes, making them promising targets for drug discovery. Though inhibition of protein-protein interactions has been challenging due to binding-site characteristics at the protein-protein interface, there has been considerable success in recent years.  Drug Discovery Chemistry Protein- Protein Interactions as Drug Targets April 29-30 2008 • La Jolla, CA  

As the level of general knowledge of proteins and protein interaction networks advances, the common understanding of a PPI [protein- protein interaction] becomes complex.  It is currently possible to define this term in a number of different ways ... At the simplest level, two discrete proteins A and B physically associate with each other in a stable complex ... Alternatively, two associating proteins might retain unaltered individual functions ... Another possibility is that a PPI may result in a loss of activity, or destruction for component A or B, or both ... Alternatively, an interaction may serve a regulatory function ... Alternatively, the interaction of A+ B may exclude A or B from interaction with another potential partner molecule. [Erica A. Golemis, Kenneth D. Tew, Disha Dadke "Protein Interaction - Targeted Drug Discovery" Biotechniques 32 (3): 636- 647, 2002]

Can be detected by yeast two- hybrids, phage display or immunoprecipitation assays.  [John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College] http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html 

A central phenomenon determining the biological pathways found in living systems.  They are the focus of many proteomic technologies being developed today to decipher an intricate network of interactions. Correlated changes in protein expression (such as co- regulation or sequential regulation) provide a hint that two proteins may be interacting with each other. Play a major role in almost all relevant physiological processes occurring in living organisms, including DNA replication and transcription, RNA splicing, protein biosynthesis, and signal transduction. 

Related terms: interaction proteomics, yeast two-hybrid.

Protein interaction databases Databases & software directory.

protein-protein interaction inhibitors: See under Proteomics categories functional proteomics

protein-RNA interactions: Can be detected by the yeast three- hybrid assay. [John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College]  http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html 

Involved in gene expression and protein synthesis.  

Related terms: interaction proteomics; Omes & omics glossary riboproteomics; Cell biology glossary  ribosome  

Related term: proteomimetics - small molecule

protein therapeutics: Molecular Medicine glossary

proteoinformatics: http://dir.niehs.nih.gov/proteomics/informtx.htm 

Google = about 11 Sept. 18, 2002; about 48 Aug, 18, 2003; about 244 July 14, 2004; about 200 Nov 10, 2006

Related term: protein informatics

proteome: The scope note  for the Journal of Proteome Research (Jan.2002) states that "primary topics will include: New approaches to sample preparation, including 2- D gels and chromatographic techniques, Advancements in high- throughput protein identification and analysis, Array- based measurements, Structural genomics data related to protein function, Research on quantitative and structural analysis of proteins and their post- translational modifications, Metabolic and signal pathway analysis, including metabolomics and peptidomics, Protein- protein, protein- DNA, and protein- small molecule interactions, Computational approaches to predict protein function, Use of Bioinformatics/ Cheminformatics to mine and analyze data, New tools in proteomic analysis, Studies on proteomics with an impact on the understanding of disease, diagnosis and medicine. Scope note, Journal of Proteome Research, American Chemical Society http://pubs.acs.org/journals/jprobs/

The importance of post- transcriptional and post- translational regulation is recognized by placing emphasis on direct knowledge of proteins and their higher- order associations in contrast to less direct inferences about proteome composition drawn from RNA measurements. Molecular Machines of Life, DOE Genomes to Life, US http://www.doegenomestolife.org/program/goal1.html

Comprehensive quantitative data on the proteins of an organism under a variety of conditions (ideally including post synthetic modifications and interactions with other molecules). To achieve this, purification each protein (including modified versions and interacting antibodies) will be an important related project  George Church Lab, Harvard- Lipper Center for Computational Genomics, 2001 http://arep.med.harvard.edu/

The concept of the proteome is fundamentally different to that of the genome: while the genome is virtually static and can be well defined for an organism, the proteome continually changes in response to external and internal events. Marc Wilkins and Denis Hockstrasser "Thinking Big Proteome Studies in a Post- Genome Era" ABRF News Dec 1996 http://www.abrf.org/ABRFNews/1996/December1996/Proteome.html

Marc Wilkins is credited with coining the word in 1994 at the Conference on Genome and Protein Maps in Siena, Italy. PROTEin complement expressed by a genOME. Wilkins et al "Progress with gene product mapping of the Mollicutes" Electrophoresis 16:1090-1094, July 1995

The dynamic nature of the proteome calls for methods to monitor, for any organism, the entire proteome's conditional state accurately and sensitively from thousands of samples. This will require greater completeness, resolution, and sensitivity than has been possible in the past using conventional imaging and gel-based technologies. Also, new tools characterizing these complexes must be developed to bridge the current size and resolution gap between single proteins suitable for high-resolution X-ray crystallographic study and the very large protein assemblies and cellular ultrastructures amenable to electron microscopy.

Wikipedia http://en.wikipedia.org/wiki/Proteome 

Proteome Society: http://www.proteome.org/  Proteome Society glossary http://www.proteome.org/4Resources/glossary.htm

Google = about 74,600 July 11, 2002; about 83,500 Sept. 18, 2002; about 159,000 Aug. 18, 2003, about 263,000 Jun 7, 2004, about 268,000 July 14, 2004, about 813,000 Aug. 15, 2005, about 7.720,000 Oct. 25, 2006

Broader terms: Genomics glossary genome;  -Omes & -omics glossary ORFeome  
Related terms: -Omes & -omics glossary translatome.  See translatome for a discussion of the ambiguities in competing definitions of proteome.

proteome chip: Microarrays & protein chips glossary

Google = about 76 Sept. 18, 2002; about 120 Aug. 18, 2003, about 208 July 14, 2004; about 1,620 Nov 10, 2006

proteome informatics: Peer Bork and David Eisenberg, "Genome and proteome informatics" Current Opinion in Structural Biology 10 (3): 341-342, 2000

Proteome Informatics group is part of the Swiss Institute of Bioinformatics (SIB). It is in charge of research and development in the fields of bioinformatics, molecular imaging and the use of Internet for biomedical applications.  Current Projects and People, ExPASy, Swiss Institute of Bioinformatics http://au.expasy.org/people/pig/ 

Google = about 261 Sept. 18, 2002; about 453 Aug. 18, 2003; about 708 July 14, 2004; about 10,700 Nov 10, 2006

proteome map: Maps, genomic & genetic glossary

Google = about 149  Sept. 18, 2002; about 319 Aug. 18, 2003; about 746 June 21, 2004; about 18,300 Nov 10, 2006 

proteome mining: Timothy AJ Haystead "Proteome Mining: Exploiting serendipity in drug discovery" Current Drug Discovery, March 2001] http://www.current-drugs.com/CDD/CDD/CDDPDF/HAYSTEAD.pdf

Google = about  68 Sept. 18, 2002; about 156 Aug. 18, 2003; about 276 June 21, 2004; about 951 Nov 10, 2006

Related term: proteome database mining:

proteomic analysis: Systematic and quantitative analysis of the properties that define protein activity and functions within a defined context, essential for biology and medicine. Ruedi Aebersold quoted in Defining the Mandate of Proteomics in the Post- Genomics Era, National Academies Press, 2002 http://www.nap.edu/books/NI000479/html/R1.html

A systematic analysis of proteins for their identify quantity and function. J Peng and Steven Gygi, Proteomics: the move to mixtures, Journal of Mass Spectrometry 35: 1083- 1091, 2001  

proteomic analysis - cells and tissue: Cell biology glossary

proteomic diagnostics: Using proteomics as a tool to diagnose diseases early on is becoming a very established way of identifying disease biomarkers. It is important to look beyond the gene expression into the interaction and functional relationships of expressed proteins and to use this information for developing new strategies for the prediction and diagnoses of diseases and their potential treatments. Proteomic tools for diagnostics May 20-21, 2008 •  Boston, MA

proteomic diversity: Alternative RNA splicing generates extreme proteomic diversity in the mammalian nervous system, where hundreds of thousands of distinct proteins are generated from approximately 30,000 genes. These protein counterparts play important roles in learning and memory, cell communication, and neural development. [Paula Grabowski, Dept. of Biological Sciences, Univ. of Pittsburgh, US, 2001] http://www.pitt.edu/AFShome/b/i/biohome/public/html/Dept/Frame/Faculty/...

Related term: RNA glossary alternative RNA splicing

Proteomic Standards Initiative PSI: PSI currently develops standards for two key areas of proteomics, mass spectrometry and protein-protein interaction data, as well as a standardised general proteomics format. Proteomic Standards Initiative, HUPO, 2005 http://psidev.sourceforge.net/ 

proteomics:  Proteomics is a rapidly evolving field that is rife with commercial opportunities as the technology achieves ever higher throughput at lower cost and greater sensitivity. Provides insights into Strengths and weaknesses of the leading technologies for protein separation, detection, and quantification - with an emphasis on high-throughput approaches The fundamental challenge posed by the vast dynamic range among protein concentrations, and the potential solutions in development and entering the market. Recent applications of proteomics to discover biomarkers for preeclampsia, and for neonatal ureteropelvic junction, and to differentiate between diagnosis of ALS and Parkinson’s disease. Technologies such as mass spectrometry, antibody-bearing chips, and solution array multiplexing to address the challenge of detecting low-abundance proteins. Insight Pharma Reports, Proteomics: Current State and Future Directions, 2006

The most useful definition of proteomics is likely to be the broadest: proteomics represents the effort to establish the identities, quantities, structures and biochemical and cellular functions of all proteins in an organism, organ, or organelle, and how these properties vary in space, time and physiological state. .. A much broader field than would be apparent from early efforts, which have focused on cataloging levels of protein expression.  Ideally it should encompass efforts to obtain complete functional descriptions for the gene products in a cell or organism.   Defining the Mandate of Proteomics in the Post- Genomics Era, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html

The systematic study of the complete complement of proteins (PROTEOME) of organisms.  MeSH 2003

The analysis of complete complements of proteins. Proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and, ultimately, their function. Initially encompassing just two- dimensional (2D) gel electrophoresis for protein separation and identification, proteomics now refers to any procedure that characterizes large sets of proteins. The explosive growth of this field is driven by multiple forces - genomics and its revelation of more and more new proteins; powerful protein technologies, such as newly developed mass spectrometry approaches, global [yeast] two- hybrid techniques, and spin- offs from DNA arrays; and innovative computational tools and methods to process, analyze, and interpret prodigious amounts of data. Stanley Fields "Proteomics in Genomeland" Science 291: 1221-1224 Feb. 16, 2001

At present, the aggregate of activities called proteomics has three distinct technical subsets: protein profiling, protein- protein interaction and structural biology. ... [producing] voluminous amounts of data ... substantial attention is now being applied to annotation methods by which the resulting information, e.g., source protein, types of  modifications, subcellular organelle, cell expression profiles, known protein interaction, protein domain organization, atom- by- atom structural coordinates, etc. can be archived in a manner amenable by computer query and in silico cross references. Robert G. Urban, ZYCOS, Inc. "Proteomics: Making sense of the census" Current Drugs 5, Aug. 2001 http://www.current-drugs.com/CDD/CDD/CDDContents-August.htm

The use of quantitative protein- level measurements of gene expression to characterize biological processes (e.g. disease processes and drug effects) and decipher the mechanisms of gene expression control. As such, proteomics focuses on the dynamic description of gene regulation and, by doing  so, offers something much more powerful than a protein equivalent of DNA databases: the concept of molecular recognition as a systematic science.  For this reason, proteomics emphasizes quantitation and the assembly of large bodies of experimental observations in numerical databases N. Leigh Anderson, Norman G. Anderson "Proteome and proteomics; New technologies, new concepts, and new words" Electrophoresis 19 (11): 1853- 1861 August 1998

Industrial scale analysis of many proteins and their interactions, over time, ultimately tying this into physiological processes and biological pathways and networks. 

The earliest PubMed reference I've found to proteomics is P James' "Protein identification in the post- genome era: the rapid rise of proteomics" Quarterly Review of Biophysics 30(4): 279- 331, Nov. 1997. References to proteomic are just a little earlier (Ian Humphery- Smith and Walter Blackstock "Proteome analysis: genomics via the output rather than the input code" Journal of Protein Chemistry16(5): 537- 544, July 1997). Perhaps earlier references can be found in the chemical and/ or biophysics literature.

Wikipedia http://en.wikipedia.org/wiki/Proteomics 

Harvard Institute of Proteomics: http://www.hip.harvard.edu/

Variant spellings without (as far as I can tell) truly variant meanings seem to distinguish proteinomics and proteonics.  I would welcome any thoughts or comments on these words. Related term proteonomics  (Or is this just another variant spelling?)

Google proteomics =   about 138,000 July 11, 2002;  about  162,000 Sept. 18, 2002; about 357,000 Aug. 18, 2003; about 776,000 June 7, 2004, about 842,000 July 14, 2004;  about 4,680,000 Aug. 15, 2005, about 10,900,000 Oct. 25, 2006

Narrower terms: Proteomics categories activity based proteomics, applied proteomics, bottom up proteomics, cell signalling proteomics, chemical proteomics, clinical proteomics, comparative proteomics, computational proteomics, differential proteomics, discovery based proteomics, drug proteomics, environmental proteomics, expression proteomics, functional proteomics, high- throughput proteomics, Human Proteomics Initiative, in silico proteomics, interaction proteomics, microbial proteomics, phyloproteomics, physiological proteomics, post- proteomics, proteomic technologies, reverse proteomics, riboproteomics, shotgun proteomics, structural proteomics, targeted proteomics, tissue proteomics, topological proteomics, toxicoproteomics

proteomics - commercialization: Covers key areas in proteomics today, including new approaches to protein expression, evolving methods of studying protein function, new technologies such as protein chips, and advances in protein informatics. Focuses on how researchers are applying new proteomic approaches to drug discovery and development, and how these technologies can be used most effectively and in a high- throughput capacity. Case studies analyzing particular applications of proteomic technologies to specific disease- related research are provided, and future trends and developments are forecast. 

proteomics technologies: Major types include protein separation, ultrafiltration, 1D and 2D gel electrophoresis, liquid chromatography, capillary electrophoresis, mass spectrometry, protein informatics, protein arrays, protein quantification, protein localization, and protein- protein interactions. 

The application of proteomics technologies to clinical research and public health in general is an immediate goal of proteomics. A distantly related goal is the eventual application of proteomics to environmental, agricultural and veterinary research, research areas that are far less developed than clinical applications. Defining the Mandate of Proteomics in the Post- Genomics Era, Board on International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html

For a field so laden with razzmatazz methods, it is striking that the number one need in proteomics may be new technology. There are simply not enough assays that are sufficiently streamlined to allow the automation necessary to perform them on a genome's worth of proteins. Those currently available barely scratch the surface of the thousands of specialized analyses biologists use every day on their favorite proteins. What we need are experimental strategies that could be termed cell biological genomics, biophysical genomics, physiological genomics, and so on, to provide clues to function. In addition, a protein contains so many types of information that each of its properties needs to be assayed on a proteome- wide scale, ideally in a quantitative manner. Stanley Fields "Proteomics in Genomeland" Science 291: 1221-1224 Feb. 16, 2001

proteomimetics-- small molecule:  The interaction between proteins is fundamental to many receptor- ligand, enzyme- substrate, and protein- protein interactions that have been linked to human disease states. Given the large number of novel protein targets emerging from the genome and the dearth of small molecules known to bind to and antagonize these targets, the challenge presented to the pharmaceutical industry is in the identification of novel agents effecting these novel targets. Traditional screening methods can be augmented by directed discovery efforts that seek to capture the essence of a protein's binding epitope in the context of a small molecule. Folding@home glossary, Stanford Univ. http://www.stanford.edu/group/pandegroup/folding/education/P.html Related term: protein small molecule interactions

Google = about 43 July 14, 2004, about 327 Oct. 25, 2006

Related term: protein small molecule interactions 

proteonomics: Expression systems that can rapidly produce high levels of recombinant proteins are a critical link between the discovery of new genes and the identification of targets and molecules for drug development. Advances in the baculovirus expression technology makes it the system of choice in the emerging field of proteonomics where rapid production and high yields of biologically active complex proteins are essential in the discovery of new drug targets, vaccines, and biotherapeutics. Folding@home glossary, Stanford Univ. http://www.stanford.edu/group/pandegroup/folding/education/P.html 

Google = about  593  Sept. 18, 2002; about 805 Aug 18, 2003; about 3,530 July 14, 2004; about 10,200 Nov. 5, 2005; about 17,300 Nov 10, 2006

Related term: proteomics  

quantitation - proteins: It is likely that in the near future, researchers will continue to use comprehensive gene arrays at the start of their work, to generate hypotheses and narrow their research questions. Then, they might delve deeper into these questions by using non-array- based gene expression studies (to get better quantitation and true relative expression) or go to a focused protein array that covers most of proteins that are indicated based on the gene array experiments.  "Proteomewide chips - not so fast" CHI's GenomeLink 21.2

regulatory homology: Quantitative analysis of protein expression data obtained by high - throughput methods has led us to define the concept of "regulatory homology" and use it to begin to elucidate the basic structure of gene expression control in vivo. [N. Leigh Anderson, Norman G. Anderson "Proteome and proteomics; New technologies, new concepts, and new words" Electrophoresis 19(11):1853-61 August 1998]

Google = about  22 Sept. 18, 2002; about 38 Aug. 18, 2003; about 49 July 14, 2004; about 144 Nov 10, 2006

reverse-two hybrid: A variation of the yeast two hybrid system, in which protein- protein interactions increase the transcription of a toxic counterselectable marker, resulting in growth inhibition. The availability of a counterselectable marker significantly extends the possibilities of the two- hybrid system. Most importantly, dissociation of  protein- protein interactions can be selected for, and thus protein- protein interactions can be characterized and manipulated genetically. [Marc Vidal et al. "The reverse two- hybrid system and several of its applications "Yeast Genetics and Molecular Biology, Madison, WI August 1996] http://genome-www.stanford.edu/Saccharomyces/yeast96/f3041.html

Google = about  197 Sept. 18, 2002; about 399 Aug. 18, 2003; about 607 July 14, 2004; about 15,700 Nov 10, 2006

riboproteomics: RNA glossary

Rosetta stone method: A way of looking at the correlation of protein domains across species. Some proteins have homologs that are fused in other species, yielding clues as to the proteins with which they might interact. In addition, proteins that have been identified in particular complexes and pathways hint at the location and function of their homologs in other species. [S. Spengler “Bioinformatics in the information age” Science 287 (5451): 221- 223 Feb. 18, 2000] 

Related term: Phylogenomics glossary phylogenetic profiles

SPR Surface Plasmon Resonance: Assays, labels, signaling & detection glossary

SWISS- PROT: Databases & software directory

sample prep: Drug discovery & development glossary

shotgun proteomics: Proteomics categories 

Google = about  39  Sept. 18, 2002; about 206 Aug. 18, 2003; about 491 July 14, 2004; about 28,500 Nov 10, 2006

single cell proteomics: Ultrasensitivity glossary 

Google = about  25 Sept. 18, 2002; about 84 Aug. 18, 2003; about 97 July 14, 2004; about 617 Nov 10, 2006

subcellular localization: Proteins glossary

subproteomes: The separation of a complex mixture of proteins is often insufficient and many protein mixtures are dominated by a few major proteins. This makes the detection of many low abundance proteins difficult or even impossible. Therefore, covering a proteome as complete as possible often requires its separation into several subproteomes.  These "functional proteomics" approaches are especially useful when looking for answers to well defined biological questions. Affinity purification of proteins, separation of organelles or multiprotein complexes that take part in certain cellular functions are good examples of these approaches. [Satu, Lehesranta, Introduction to Proteomics, Dept. Biochemistry, Univ. of Kuopio, Finland, 2001] 

Proteins found in a specific tissue, cell type or body fluid (may incorporate a temporal aspect as well.  

Google = about  35 Sept. 18, 2002; about 76 Aug. 18, 2003; about 217 July 14, 2004; about 9,840 Nov 10, 2006

systems biology: Genetic manipulation & disruption glossary

top-down mass spectrometry: Mass spectrometry glossary

toxicoproteomics: Pharmacogenomics glossary

Google = about  96 Sept. 18, 2002; about 261 Aug. 18, 2003; about 634 July 14, 2004; about 16,400 Nov 10, 2006

two-D gel electrophoresis: See 2D gel electrophoresis

two hybrid: See yeast two hybrid

two hybrid system techniques: Screening techniques used to identify genes encoding interacting proteins. Variations are used to evaluate complex interplay between proteins and other molecules. MeSH, 2000

whole proteome: Proteome analysis has become indispensable and complementary to genomic analysis. With access to whole genome sequences from various organisms and with the imminent completion of many more, the SWISS- PROT group at EBI has developed a research- oriented initiative that utilises many of the existing resources and provides comparative analysis of the predicted protein coding sequences of all complete genomes. [Rolf Apweiler "Whole Proteome Analysis: The role of InterPro and CluSTr" Plant & Animal Genome IX, San Diego CA  Jan. 13-17, 2001] http://www.intl-pag.org/pag/9/abstracts/W22_01.html

Google = about  259 Sept. 18, 2002; about 586 Aug. 18, 2003; about 1,610 July 14, 2004; about 30,600 Nov 10, 2006

whole proteome interaction mining: A major post- genomic scientific and technological pursuit is to describe the functions performed by the proteins encoded by the genome. One strategy is to first identify the protein- protein interactions in a proteome, then determine pathways and overall structure relating these interactions, and finally to statistically infer functional roles of individual proteins. Although huge amounts of genomic data are at hand, current experimental protein interaction assays must overcome technical problems to scale- up for high- throughput analysis. In the meantime, bioinformatics approaches may help bridge the information gap required for inference of protein function. JR Bock, DA Gough, Whole- proteome interaction mining, Bioinformatics 19(1) :125- 134, Jan. 2003

yeast localizome: See under Proteins glossary protein localization

yeast one hybrid: A variant of the  yeast two- hybrid system, which identifies DNA- binding proteins from cDNA libraries or known gene sequences. 

Google = about  542 Sept. 18, 2002; about 1,290 Aug. 18, 2003; about 2,260 July 14, 2004; about 45,800 Nov 10, 2006

Related term:  protein- DNA interactions

yeast three hybrid: The three-hybrid system enables the detection of RNA- protein interactions in yeast using simple phenotypic assays. It was developed in collaboration with Stan Fields laboratory (University of Washington- Seattle). Original publication of the method [D. SenGupta, B. Zhang, B. Kraemer, P. Prochart, S. Fields and M. Wickens. 1996. A three- hybrid system for detecting RNA- protein interactions. Proc. Natl. Acad. Sci. 93, 8496- 8501] http://www.biochem.wisc.edu/wickens/3H/3HybrdSys_SenGupta.pdf [Marvin Wickens, Dept. of  Biochemistry,. Univ. of Wisconsin] http://www.biochem.wisc.edu/wickens/3H/

Modification of yeast two hybrid system. The third hybrid may be a first one with an RNA or with a small molecule that is a cell permeable chemical inducer of dimerization.  

Google = about 192 Sept. 18, 2002; about 603 Aug. 18, 2003, about 812 July 14, 2004; about 24,000 Nov 10, 2006

Related term  protein- RNA interactions.

yeast two hybrid: An approach to studying protein- protein interactions. The basic format involves the creation of two hybrid molecules, one in which a "bait" protein is fused with a transcription factor, and one in which a "prey" protein is fused with a related transcription factor. If the bait and prey proteins indeed interact, then the two factors fused to these two proteins are also brought into proximity with each other. As a result, a specific signal is produced, indicating an interaction has taken place. 

A system first developed in 1989 (by Stan Fields and colleagues) to identify proteins (and their genes) that interact with known proteins. 

Google = about  11,700 Sept. 18, 2002; about 36,400 Aug. 18, 2003, about 81,700 July 14, 2004; about 836,000 Nov 10, 2006

Interaction Trap at Work, Ilya Serebriiski, Fox Chase Cancer Center, US http://www.fccc.edu/research/labs/golemis/InteractionTrapInWork.html

Related terms: dissociator assays, reverse two hybrid, two hybrid system techniques, bait, prey

Bibliography
Insight Pharma  Proteomics: Current State and Future Directions, 2006
CHI Proteins: Strategies for Optimizing Drug Discovery report, 2004
Folding@home glossary, Stanford Univ. Tug Sezen, Vijay Pande, 2002, 200+ definitions http://www.stanford.edu/group/pandegroup/folding/education/glossary.html
National Academy of Sciences, Defining the Mandate of Proteomics in the Post- Genomics Era,  2002 http://www.nap.edu/books/NI000479/html/R1.html
National Academy of Sciences, Technology, Science and Economic Policy Board, Workshop on Exploring Patent and Licensing  Policy for Proteomics, June 2004 http://www7.nationalacademies.org/step/Proteomics_June_transcript.pdf  
Nature, “Post-Genomics Gateway” http://www.nature.com/genomics/post-genomics/index.html
Nature Proteomics, Mar 2003 http://www.nature.com/nature/insights/6928.html 
Nature, "Proteomics in action"  http://www.nature.com/genomics/post-genomics/action.html
Nature Reviews Proteomics, 2005   http://www.nature.com/reviews/focus/proteomics/index.html 
UNI-PROT KnowledgeBase keywords,  Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, PIR Protein Information Resource, 2007 http://beta.uniprot.org/keywords/ 

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