Applications  Map: Finding guide to terms in these glossaries  Site Map
Related glossaries include Proteomics, Proteins, Protein categories, Protein Structures, Structural genomics

absolute proteomics:  Nature Biotechnology 23(5): vii, May 2005

activity based protein profiling:   

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

Related terms: Drug discovery & development, Targets

biochemical proteome: An analysis of the genomic sequences of many organisms indicates that a large fraction of the encoded proteins cannot be assigned particular molecular and/or cellular functions. Since the molecular function of a gene product is tightly coupled to its three-dimensional structure, determining the structure or its folding pattern may provide important insight into its molecular function, which, in turn, may help to place it in a particular cellular pathway. However, structure determination and the experimental verification of the molecular function inferred by the structure require cloning and expression of the genes, and purification of the proteins in the proteome, the protein complement of a genome. Biochemical and molecular biological approaches are used to develop high throughput methods for determining structure- function relationship of a proteome. Rosalind Kim, Physical Biosciences Division, Lawrence Berkeley National Lab, US http://www.lbl.gov/pbd/about/people/kim-r.htm

biochemical proteomics: 

Google = about 25 Sept. 10, 2003; about 140 Nov 13, 2006

bottom up proteomics: 

cardioproteomics:  Proteins differentially  expressed in normal and failing human hearts. Cardiogenomics, Myogen, US http://www.myogen.com/discovery/cardio.php  

Google = about 8, Sept. 10, 2003

cell signalling proteomics:  

chemical proteomics, chemiproteomics: Chemistry & biology glossary  
chemoproteomics: -Omes & -omics glossary

clinical proteomics: Molecular Medicine glossary

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 Functional Genomics glossary 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]

Google - about 1,290 Sept. 10, 2003

differential proteomes: 

Google - about 169 Sept. 10, 2003, about 38 Apr 10 2007

differential proteomics: Differential proteomics makes qualitative and quantitative comparisons of proteomes under different conditions. This knowledge enables us to unravel the mysteries of biological processes. Genencor Proteome and Tools http://www.genencor.com/cms/connect/genencor/technology/protein_chemistry/proteomics/proteome_and_tools/proteome... 

Google = about 14,000 Apr 10, 2007

differential subproteomes: As defined by relative solubilities, cellular location and narrow-range immobilised pH gradients. . SJ Cordwell, AS Nouwens, NM Verrills, DJ Basseal, BJ Walsh, Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two-dimensional electrophoresis gels, Electrophoresis, 21(6): 1094- 103, April 2000

Google = about 4 Nov 5, 2005; about 3 Apr 10, 2007

discovery based proteomics:  

environmental proteomics:  

expression proteomics: Expression glossary

functional 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. 

Google = about 8,480  Feb. 4, 2004

See also activity based protein profiling

glycoproteomics: Glycosciences glossary

Google - about 282 Sept. 10, 2003

high- throughput proteomics:

Human Plasma Proteome: Proteomics glossary

in silico proteomics: In silico & Molecular modeling glossary 

Google - about 46 Sept. 10, 2003

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]  http://pubs.acs.org/journals/mdd/toc/0900toc.html

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

Related/equivalent term?: interaction proteomics

interactome, interactomics: Omes & omics glossary

kinase proteomics:

location proteomics: Seeks to provide automated, objective high-resolution descriptions of protein location patterns within cells. Methods have been developed to group proteins into statistically indistinguishable location patterns using automated analysis of fluorescence microscope images. ... Preliminary work suggests the feasibility of expressing each unique pattern as a generative model that can be incorporated into comprehensive models of cell behaviour. RF Murphy, Location proteomics: a systems approach to subcellular location, Biochem Society Transactions, 33 (Pt 3): 535- 538, June 2005

Google - about 344 Sept. 10, 2003; about 525 March 14, 2006

membrane proteomics: Membrane proteins comprise the largest set of proteins to resist high-throughput structural genomics efforts. One of the major impediments to the analysis of membrane proteins is the lack of generic and effective expression systems. The aims of the membrane protein platform are to develop the methodologies to perform high-throughput cloning, expression, purification and crystallization of membrane proteins.

To date, we have purified over 30 targets to homogeneity. This represents ~10% of the total number of genes cloned (compared to an average of 40% for similar efforts with soluble proteins). The proteins we have purified include several active prokaryotic and eukaryotic rhomboid proteases and human G protein-coupled receptors (GPCRs).  "Membrane Proteomics", A Edwards Labs, Univ. of Toronto, Canada, 2004  http://www.utoronto.ca/AlEdwardsLab/membrane_proteomics_index.html 

Membrane proteins perform some of the most important functions in the cell, including the regulation of cell signaling through surface receptors, cell-cell interactions, and the intracellular compartmentalization of organelles. Recent developments in proteomic strategies have focused on the inclusion of membrane proteins in high-throughput analyses. While slow and steady progress continues to be made in gel-based technologies, significant advances have been reported in non-gel shotgun methods using liquid chromatography coupled to mass spectrometry (LC/MS).  Wu CC, Yates John R,  The application of mass spectrometry to membrane proteomics Nature Biotechnology 21(3): 262- 267, March 2003

Google = about 25,300 March 1, 2006

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

Google - about 182 Sept. 10, 2003

Related term: Omes & omics glossary microbiome

microorganism proteomes: Drug discovery & development glossary see under vaccine antigen discovery

microproteomics:

Google - about 29 Sept. 10, 2003; about 43 May 9, 2005

mitochondrial proteome:

molecular proteomics: Studying the interactions of proteins with other proteins and cellular components.  [Backgrounder: Human Genome Technology, Indiana Genomics Initiative, Indiana Univ. US, 2002] http://www.ingen.iu.edu/faq/backgrounders.html

Google - about 377 Sept. 10, 2003; about 205 June 15, 2007

Related/equivalent term?: interaction proteomics

neuroproteomics: Protein profiling related to CNS cells, tissues and neurodegenerative and neuropsychiatric conditions. 

Google - about 386 Sept. 10, 2003

pharmacoproteomics:   Pharmacogenomics glossary.

Google - about 399 Sept. 10, 2003

phosphoproteome: Characterization of post- translational modifications in proteins is one of the major tasks that is to be accomplished in the post- genomic era. Phosphorylation is a key reversible modification that regulates enzymatic activity, subcellular localization, complex formation and degradation of proteins. DE Kalume et. al, Tackling the phosphoproteome: tools and strategies, Current Opinion in Chemical Biology 7(1): 64- 69, Feb. 2003

Ahn NG, Resing KA (2001) Toward the phosphoproteome. Nature Biotechnology 19:317- 19318 

Google = about 88 Sept. 19, 2002; about 773 June 18, 2004; about 3,600 Feb. 14, 2005, about 1,070 Oct. 25, 2006

phosphoproteomics: Developments in the field of phosphoproteomics have been fueled by the need simultaneously to monitor many different phosphoproteins within the signaling networks that coordinate responses to changes in the cellular environment. Marc Mumby, Deirdre Brekken, Phosphoproteomics: new insights into cellular signaling, Genome Biology 2005, 6:230     doi:10.1186/gb-2005-6-9-230

Google = about 6,030 Aug. 15, 2005, about 39,400 Oct. 25, 2006

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

Google = about 15 July 11, 2002; about 24 July 14, 2003; about 46 June 7, 2004, about 64 Aug. 15, 2005, about 84 Nov 5, 2005, about 158 Oct. 25, 2006

physiological proteomics:  Proteomics relying on two- dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is an excellent experimental tool for physiological studies opening a new perspective for understanding overall cell physiology. This is the intriguing outcome of a method introduced by Klose and O'Farrell independently 25 years ago. Physiological proteomics requires a 2-D reference map on which most of the main proteins were identified. ...  A big challenge for future studies is to provide an experimental protocol covering the fraction of intrinsic membrane proteins that almost totally escaped detection by the experimental procedure used in this study. [K. Buttner et. al. A comprehensive two- dimensional map of cytosolic proteins of Bacillus subtilis Electrophoresis. 22(14):2908-2935, 2001 Aug.] 

post-proteomics: Proteomics glossary

"predictive proteomics": Pseudo- gel construction from open reading frames. [ From Genome to Proteome 4th Siena Conference, Sept. 4-7, 2000, Electrophoresis Society Newsletter 6(1), Jan.2001]  http://www.aesociety.org/AESnews.html

protein pulldowns: High- throughput analyses afforded by mass spectroscopy require sample preparation processes that can keep pace. Standardization and automation of protein “pulldowns”, and related reagents are being developed. The processes are designed to provide a straightforward material flow in high- throughput format for the pulldown of protein complexes from the Rhodopseudomonas palustris and Shewanella oneidensis genomes. Existing techniques are well developed; however, some processes in clone library, antibody, and protein complex production have never been automated and few established protocols are available.  P.R. Hoyt,  Automation of Protein Complex Analyses in Rhodopseudomonas palustris and Shewanella oneidensis, DOE, Genomes to Life, 2003 http://doegenomestolife.org/pubs/2003abstracts/html/GTL.htm

proteomics: Industrial scale analysis of many proteins and their interactions, over time, ultimately tying this into physiological processes and biological pathways and networks. More under proteomics: Proteomics glossary

quantitative proteomics: The use of stable isotopes as internal standards in mass spectrometry has opened a new era for quantitative proteomics. Depending on the point at which the label is introduced, most procedures can be classified as in vivo labeling, in vitro pre- digestion labeling or in vitro post- digestion labeling. In vivo labeling has been used for cells that can be grown in culture and has the advantage of being more accurate. The pre- digestion and post- digestion labeling procedures are suitable for all types of sample including human body fluids and biopsies. Several new mass spectrometric strategies mark significant achievements in determining relative protein concentrations and in quantifying post- translational modifications. Quantitative proteomics using mass spectrometry, S Sechi, Y. Oda Current Opinion in Chemical Biology 7(1): 70- 77 Feb 2003 

reverse chemical proteomics: Chemistry & Biology glossary

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. Marc Vidal, AJ Walhout, "Protein Interaction Maps for Model Organisms" Nature Reviews Molecular Cell Biology 2; 55- 63, Jan. 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"]  

riboproteomics: Omes & omics 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

Allows complete bypassing of  2D-gel electrophoresis. Resembles shotgun genome sequencing. Proteins are broken  apart, then the peptides are sequenced, and  reassembled. The process is made much easier by the sequencing of the human genome, and the more complete that sequence is, the stronger the approach is. Shotgun proteomics is enabled by multidimensional protein identification technology (MudPIT). [John Yates in CHI Proteomics Update report]

structural proteomics: Structural genomics glossary

Google - about 4,610 Sept. 10, 2003

subcellular proteomics: See under subproteomics

Google = about 903 Nov 5, 2005

subproteomics: Advances in the field of proteomics have made it possible to search for differences in protein expression between AM [alveolar macrophages] and their precursor monocytes. Proteome features of each cell type provide new clues into understanding mononuclear phagocyte biology. In-depth analyses using subproteomics and subcellular proteomics offer additional information by providing greater protein resolution and detection sensitivity. HM Wu, M Jin, CB Marsh, Toward functional proteomics of alveolar macrophages, Am J Physiol Lung Cell Mol Physiol. 288(4): L585- 595, April 2005 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15757951&query_hl=42

Subproteomics, utilising up to 40 two-dimensional gels per sample will become a powerful tool for near- to- total proteome analysis in the postgenome era. Furthermore, this new approach can direct biological focus towards molecules of specific interest within complex cells and thus simplify efforts in discovery- based proteome research. SJ Cordwell, AS Nouwens, NM Verrills, DJ Basseal, BJ Walsh, Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two- dimensional electrophoresis gels, Electrophoresis, 21(6): 1094- 103, April 2000 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10786883&query_hl=42

Google = about 265 Nov 5, 2005

subtractive proteomics:  Molecular Imaging, Jan Schnitzer, Nov. 2004

Google = about 130 June 29, 2004

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

Google - about 365 Sept. 10, 2003

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

Google - about 303 Sept. 10, 2003

topological proteomics: 

toponomics:  Management and interpretation of high- throughput experiments analysing protein networks of whole cells in situ, also known as topological proteomics or toponomics. MelTec generates continuously large data sets to decipher the toponome of cells and tissues by tracing out and interpreting the context of proteins in cells. management and interpretation of high- throughput experiments analysing protein networks of whole cells in situ. FIT and MelTec GmbH Form Alliance to Create Next-Generation IT Platform for Topological Proteomics, press release, 2003 http://www.fit.fraunhofer.de/medien/meltec/pm_2003-1-20.html 

Google = about 1,090 Oct. 25, 2006

toxicoproteomics: Pharmacogenomics glossary

Google - about 356 Sept. 10, 2003

Bibliography
Nature “Post-Genomics Gateway” http://www.nature.com/genomics/post-genomics/index.html
UNI-PROT KnowledgeBase keywords http://www.expasy.org/cgi-bin/keywlist.pl   Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, PIR Protein Information Resource, 2004, 800 + definitions.

Alpha glossary index 

How to look for other unfamiliar  terms

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