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Related glossaries include Applications overview: Functional genomics, Structural Genomics

 Informatics overview: Algorithms & data management, Molecular Modeling, 

Technologies overview Chromatography & electrophoresis,    Mass spectrometry,  Microarrays,  

Biology overview: Expression, Proteins, Protein Structure. 

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

activity based proteomics: Identification and analysis of changes in active proteins in different cell types and under different conditions ... addressing the biochemical mechanisms of disease more directly than standard genomics and proteomics techniques. [ActivX website "About Precision Proteomics']  http://www.activx.com/about.htm 

annotation- proteins: 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

applied proteomics: Current applications of proteomics seem to be focusing on toxicology and drug target identification.  

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. [CHI Proteomics]

biological atlas: Maps, genomic & genetic glossary

cell mapping: Maps genomic & genetic

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

chemical microarrays: Microarrays glossary

chemical proteomics: To link new proteins with known catalytic activities, proteome- scale screens for generic enzyme activities (e.g. protease and phosphatase) should be implemented ... Although it is impossible to screen for chemical reactions that are unknown, in theory, identifying small molecules that bind to the new proteins may elucidate clues to new activities. These ligands might be found by screening the new proteins against diverse chemical libraries using existing methods such as NMR spectroscopy, microcalorimetry, or microarrays. The general concept of ascribing function to new proteins by discovering small molecule ligands might be referred to as chemical proteomics. [Aled Edwards et al. “Proteomics: new tools for a new era” Modern Drug Discovery 3 (7): 35-44 Sept. 2000] Related terms biochemical genomics Genomics glossary; chemical genomics Drug discovery & development

comparative proteomics: The C. elegans proteome was used as an alignment template to assist in novel human gene identification … Among the available 18,452 C. elegans protein sequences, our results indicate that at least 83% had human homologous genes, with 7954 records of C. elegans proteins matching known human gene transcripts. [CH Lai et al "Identification of Novel Human Genes Evolutionarily Conserved in Caenorhabditis elegans by Comparative Proteomics" Genome Research 10(5): 703-713 May 2000] Related terms comparative genomics, evolutionary genomics.

computational proteomics: Large- scale generation and analysis of 3D and 4D protein structural information and the application of structural knowledge across all life science disciplines. [Edward T. Maggio, Kal Ramnarayan "Recent developments in computational proteomics" Trends in Biotechnology 19 (7): 266- 272 July 2001]

DNA protein interactions: See protein- DNA interactions

differential labeling: Assays, labeling, signaling & detection glossary

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

evolutionary homology:  Functional genomics glossary

Expressed Protein Tags EPTs: Multi- cellular organisms have been evolving a system with which they can discriminate between cells of their own origin and other adventitious cells or cells which have been infected with intracellular pathogens. To achieve this goal, a family of receptors, known as multi- ligand receptors (MLR), have evolved to be remarkably promiscuous binders of peptide ligands. The MLR-bound ligands are derived from degradation intermediates of cellular proteins. Typically, these ligands are 8-12 amino acids in length and have been coined by CANVAS as "expressed protein tags" or EPTs. EPTs are of sufficient length to differentiate particular proteins and/ or individual genes. Each MLR has a single binding site and thus contains a single EPT copy.  [Canvas Informatics, Inc, "Technology" 2001] http://www.canvas-informatics.com/tech.html

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://currentdrugdiscovery.com/CDDPDF/issue%205/Urban.pdf

Related term: EST expressed sequence tags: Sequences, DNA & beyond

expression proteomics: Expression glossary

Fluorescence Resonance Energy Transfer FRET: Assays, labels, signaling & detection glossary

functional cloning: Functional genomics glossary In-depth

functional glycomics: At the present time approximately 110 glycogenes which encode glycosyltransferases and related genes have been cloned. Even though some of the biological functions of those genes have been elucidated, most of the actual functions of these genes continue to be obscure, and limited information is available in terms of their pathophysiolgical significance. Therefore in order to clarify the functional significance of these genes, one of the major strategies is focused on the identification of likely target molecules in vivo and the identification of their functional significance. Knock out or transgenic mice have already been reported for several glycogenes and currently available information indicate that some are lethal and some lead to interesting phenotypic changes. [Naoyuki Taniguchi "Beyond glycogenes" Glycoforum, Japan 2001] http://www.glycoforum.gr.jp/science/glycogenes/BG01/BG01E.html

functional proteomics: Relating function to gene expression,  protein- protein interactions. [CHI Proteomics] 

Is yielding large databases of interacting proteins and extensive pathways maps of these interactions are being scored and deciphered by novel high throughput technologies. However, traditional methods of screening have not been very successful in identifying protein- protein interaction inhibitors. [CHI Summit Proteomics]

The identification and measurement of changes in concentration of specific proteins that cells make as a result of their genetic response to specific toxicants and how these proteins are related  [NIEHS, US "National Center for Toxicogenomics to Study Genetic Basis of Disease Caused by Environmental Pollution" Dec. 7, 2000] http://www.niehs.nih.gov/nct/pr07de00.htm

guilt by association: Expression glossary

Hidden Markov Models HMM: Molecular modeling glossary

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: Functional Genomics

homology: Functional Genomics

homology modelling: Structural genomics glossary

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.. Human Proteome Project: PepTalk Jan. 9-11 2002 San Diego CA  

HUPO Human Proteome Organisation website: http://www.hupo.org/

Human Proteomics Initiative: http://www.expasy.ch/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. 

in silico proteomics: Molecular modeling glossary 

interaction proteomics: Protein- protein interactions lie at the heart of most cellular processes … A complete understanding of cellular function depends on a full characterization of the complex network of cellular protein- protein associations …. Alternative proteomics technologies are being developed to complement the two- hybrid system. These methods reveal direct protein- protein interactions by using protein affinity chromatography. Protein affinity chromatography, as developed by Greenblatt, Alberts, and colleagues, has the disadvantage of requiring purified proteins as reagents, but it is superior to the two- hybrid approach because it generates fewer false positives and is more amenable to high- throughput screening. [Aled Edwards et al. “Proteomics: new tools for a new era” Modern Drug Discovery 3 (7): 35-44 Sept. 2000] 

Related terms  protein- DNA interactions, protein- protein interactions, protein- RNA interactions, reverse two- hybrid, yeast one- hybrid, yeast- two hybrid; yeast three- hybrid In-depth co- precipitation, co- immunoprecipitation; Maps genetic & genomic  cell mapping, maps- protein, peptide mapping, protein interaction mapping, protein linkage maps; Omes & omics glossary interactome

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]

localizome: Omes & omics glossary

localizome mapping: Maps, genomic & genetic glossary

membrane proteins: Protein structure glossary

microbial proteomics:  Bacterial genomes encode all possible virulence determinants, vaccine candidates, and potential drug targets. Further, a completed genomic sequence establishes a basis for high throughput analysis of the proteins expressed (i.e., the proteome). Respiratory pathogens have been among the first to have their genomes entirely sequenced.

Mycoplasma pneumoniae harbors the second smallest genome of any self-replicating life form and encodes 679 putative proteins. These genome- predicted proteins will be correlated with those actually present, detecting any biological event that generates a protein of different molecular composition than that predicted. These include sequence or reading frame errors, imprecise bioinformatics, co- or post- translational modifications, and mutational or proteolytic strategies for antigenic variation. [Neil Kelleher "Enzymology and Proteomics" Dept. of Biochemistry, Univ. of Illinois - Urbana Champaign, US, 2000] http://www.scs.uiuc.edu/~bioch/kelleher.html

Related term: Omes & omics glossary microbiome

ORFeome: Omes & omics glossary

peptide mapping: Maps, genomic & genetic

peptidomics: Omes & omics glossary

perturbagens: Peptides, which disrupt key protein-protein interactions. [CHI Proteomics]

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

phage display: Functional genomics glossary

pharmacoproteomics: Pharmacogenomics glossary.

phylogenetic profiles: Functional genomics glossary

phyloproteomics: Identification of unknown bacterial isolates based on similarities within protein biomarker databases. [Gregory C. Conway et. al. "Phyloproteomics: Species Identification of Enterobacteriaceae Using Matrix- Assisted Laser Desorption/ Ionization Time- of- Flight Mass Spectrometry" J. Mol. Micro. Biotechnol. 3: 103-112, 2001 ] http://www.jmmb.net/abstracts/v3/v3n1/10.html 

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.

prey: See under bait.

protein: Proteins glossary

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

protein arrays: Microarrays glossary

protein- carbohydrate interactions: Are now recognized to be important mediators of cell communication. In the last decade many novel carbohydrate binding proteins (CBPs) have been described, and several have been documented to play critical roles in cell trafficking and cell signaling. Despite these advances, the rate of generating new information has been slow, and the biological roles of most mammalian CBPs remain poorly understood. While the importance of this field has attracted many outstanding laboratories, a major barrier to rapid progress has been the structural complexity and heterogeneity of the carbohydrates themselves, and the analytical and synthetic challenges this poses. A further complexity arises from the fact that carbohydrate ligands are post-translational modifications of proteins and lipids whose synthesis is directed by the coordinated expression of multiple genes in a manner that is not template driven. [Consortium for Functional Glycomics, "Overview of the Program" US, 2001]http://glycomics.scripps.edu/program.html

protein chips: Microarrays 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 interaction proteomics

protein databases: 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 term protein identification

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. [CHI Structural proteomics]

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

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

protein expression mapping: Maps, genomic & genetic glossary

protein expression profiling: Expression glossary

protein function: 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]

Moving from functional genomics to the correlation of function(s) with proteins. Intriguing tools are beginning to emerge. [CHI Proteomics]

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

Related terms interaction proteomics;  cell mapping; gene function Functional genomics glossary.

protein identification: Related term protein databases

protein informatics: Includes bioinformatics technology to cross reference protein informatics with genomic databases, sequence data of protein fragments by mass spectrometry and identification of these fragments using more remote relationships; construction and management of international protein structural databases; protein profiling and characterization data handling; data that elucidates the relationship between structures and functions of biological macromolecules by X-ray crystallography, large scale molecular simulation and structural bioinformatics, protein structure data handling and storage, structural bioinformatics covering molecular modeling and design; protein array and chip data handling; development of new algorithms and software for large scale simulation calculations by parallel computers; protein- protein interaction data and libraries; protein structure data determination by X-ray crystallography and development of automatic analysis systems; protein expression databases; automated technology for high- throughput protein function assignment and annotation. Protein Informatics November 12-13, 2001, San Diego, CA

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]

protein interaction: See interaction proteomics, protein- DNA interactions, protein- protein interactions, protein- RNA interactions.

protein interaction mapping: Maps genomic & genetic 

protein linkage maps: Maps genomic & genetic  

protein microarrays: Microarrays glossary

protein profiling: Expression glossary

protein- protein 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. [CHI Proteomics] 

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. [CHI Summit Proteomics]

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 

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 see Databases & software directory.

protein-protein interaction inhibitors: See under functional proteomics

protein knockouts: Our proteomics efforts are focused largely on developing new techniques to probe protein- protein interactions and to construct devices that allow one to monitor the levels and post- translational modification states of hundreds or even thousands of proteins simultaneously. A third major goal is to develop “protein knockout” methods that would allow researchers to rapidly develop reagents to block one or more functions of a newly discovered protein to facilitate studies of its role in cellular metabolism. [Thomas J. Kodadek, Internal Medicine and Molecular Biology, Univ. of Texas Southwestern Graduate Biomedical School, 2001]   http://www2.utsouthwestern.edu/gradschool/webrib/kodadek.htm

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] Related term interaction proteomics http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html 

Involved in gene expression and protein synthesis.  

Related terms:  riboproteomics In-depth; ribosome (Cell biology glossary)

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. http://pubs.acs.org/journals/jprobs/

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. [Wilkins and 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]

Related terms Omes & omics glossary orfeome, translatome.  See translatome for a discussion of the ambiguities in competing definitions of proteome.

proteome chip: Microarrays glossary

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. [ExPASy, Swiss Institute of Bioinformatics] http://www.expasy.ch/people/PI_group.html

proteome map: Maps, genomic & genetic glossary

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

proteomics: 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]

The proteomic pipeline is under way to reveal and identify and understand biological mechanisms that exist between proteins, protein folding and how protein structure relates to function. This explosion in genomic and proteomic data, the exponential increase of known protein structures should make it easier to develop highly specific, safer and more effective pharmaceuticals. Cambridge Healthtech Institute's Proteomics Europe is designed to provide in- depth coverage of the accelerating diagnostic and therapeutic product development, integration of databases, storage/ retrieval, analysis, data mining and manipulation of biological sequence, structure, function and annotation data Proteomics Europe: Proteins to Profits March 25-27, 2002, Munich, Germany

In-depth coverage of the high- throughput protein expression analysis and characterization field, as well as its impact on diagnostic and therapeutic product development. Proteomics: Beyond genome June 6- 7, 2002, San Diego CA

The study of proteins that are encoded by the genes of an organism (or of a cell or tissue in a multicellular organism). Such study includes determining protein expression (identifying and quantifying the proteins expressed), characterizing the protein (e.g., assessing post- transitional modification), determining protein function. Studying protein interactions, and exploring the correlation of these proteins with disease. [CHI Proteomics] 

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]

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):1853-61 August 1998]

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?)

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. [CHI report, Profiting from Proteomics: High Throughput Expression, Functional Proteomics, Protein Chips, and Protein Informatics, Jan. 2002]    http://www.chireports.com/content/reports/proteomics2.asp

proteomics technologies: 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]

Although automation is being applied to what has traditionally been the workhorse of protein analysis – 2D gel electrophoresis – many limitations remain as to the speed, sensitivity and  reproducibility of this decades old method. [CHI Summit Proteomics] Mass spectrometry is also gaining in importance. Related terms Microarrays protein chips, protein microarrays

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. [Manon M.J. Cox "Baculovirus Expression System: System of Choice for Novel Proteins" Protein Sciences Corp. CHI Protein Expression, Mar. 8-10, 2000]  http://www.healthtech.com/conference/00pex/pex.htm  Related term proteomics Is this truly a different term?

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]

reverse proteomics: In reverse proteomics, the starting point is the DNA sequence of the genome of an organism. First, the transcriptome (complete set of transcripts) and proteome (complete set of proteins) are predicted in silico and subsequently this information is used to generate reagents for their analysis. ["Protein Interaction Maps for Model Organisms" Nature Reviews Molecular Cell Biology 2; 55-63 (2001) ] http://www.nature.com/nrm/journal/v2/n1/slideshow/nrm0101_055a_F2.html

Compounds can be tested to see if they can disrupt protein - protein interactions - a strategy that may be extremely useful for the development of new drugs. [Wellcome Trust, UK "The Human Genome Functional Genomics" ] http://www.wellcome.ac.uk/en/genome/futscifun.htm

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

riboproteomics: Omes & omics 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 phylogenetic profiles. Functional genomics glossary

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

SWISS- PROT: Databases & software directory

sample prep: Drug discovery & development glossary

shotgun proteomics: Dirk Wolters et. al, "An Automated Multidimensional Protein Identification Technology for shotgun proteomics "Analytical Chemistry 35 (23): 5683-5690, Dec. 1, 2001

structural proteomics: Structural genomics glossary

Tandem Affinity Purification TAP: A generic and rapid method being developed at EMBL to recover proteins that are present in the cell even at very low concentrations, utilizing a "TAP tag" [CHI Summit Proteomics]

targeted proteomics: Biochemical approaches to proteomics, particularly using mass spectrometry.

tissue proteomics: The National Cancer Institute and the Food & Drug Administration are funding a multimillion dollar ''Tissue Proteomics Initiative'' to identify proteins linked to early stages of colon, breast, and other cancers. ["Beyond the genome" Business Week Online, April 10, 2000] http://www.businessweek.com/2000/00_15/b3676117.htm

toxicoproteomics: Study of  global protein expression to better understand toxicology.

two-D gel electrophoresis: See 2D gel electrophoresis

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

yeast one hybrid: Variation on yeast two hybrid system, used for detecting protein- DNA interactions. [Yeast Hybrid Technologies, Li Zhu, editor, BioTechniques, 2000] See also DNA- protein interactions. http://shop.store.yahoo.com/biotechniques/yeashybmet.html

yeast three hybrid: 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. [CHI Proteomics] 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. [CHI  Breaking Bottlenecks]

A system first developed in 1989 (by Stan Fields and colleagues) to identify proteins (and their genes) that interact with known proteins. [CHI Proteomics] Related terms dissociator assays, reverse two hybrid; In-depth bait, prey

Bibliography

[CHI Summit Proteomics] Proteomics: Analysis of Selected Emerging Technologies, Editor: Mike Silver, Cambridge Healthtech Institute, Jan. 2001  

[CHI Proteomics] , Proteomics: A Key Enabling Tool for Genomics? Cambridge Healthtech Institute, Malorye Branca and Lucy J. Sannes Genomic Pathways Report 1, 1999 

[CHI Update Proteomics] Profiting from Proteomics: High-Throughput Expression, Functional Proteomics, Protein Chips, and Protein Informatics, January 2002 http://www.chireports.com/content/reports/proteomics2.asp

Nature “Post-Genomics Gateway” http://www.nature.com/genomics/post-genomics/index.html

Alpha glossary index

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.