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Protein Technologies glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions?  Mary Chitty 
mchitty@healthtech.com
Last revised November 08, 2013
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2D gel electrophoresis: A key technology for proteomics. Chromatography & electrophoresis glossary

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

antibody display:  de Kruif J,, Boel E, Logtenberg T. Selection and application of human single chain Fv antibody fragments from a semi-synthetic phage antibody display library with designed CDR3 regions. J Mol Biol. 1995 Apr 21;248 (1): 97-105, April 1995 .  

antibody microarrays:  While transcriptional profiling provides invaluable insight into biological function on a genome- wide scale, it doesn't offer information on regulation that occurs at the protein level (e.g., degradation, phosphorylation/ dephosphorylation, sub- cellular localization, etc.). We are investigating the possibility of using microarrays of antibodies to study regulation at the protein level. Harvard Center for Genomic Research, MacBeath Lab] http://www.cgr.harvard.edu/macbeath/index.html
Related terms: protein arrays, protein chips, protein microarrays   Wikipedia  http://en.wikipedia.org/wiki/Antibody_microarray 

aptamers: Technologies overview

bacteriophage: Many phage have proved useful in the study of molecular biology and as vectors for the transfer of genetic information between cells lambda bacteriophage can also undergo a lytic cycle or can enter a lysogenic cycle, in which the page DNA is incorporated into that of the host, awaiting a signal that initiates events leading to replication of the virus and lysis of the host cell. Glick

The workhorse of phage display is the M13 bacteriophage virus. Related terms: phage, phage display bacteriophage, biopanning, phage;  Labels, signaling & detection     Proteomics directed protein evolution

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.

biopanning: Encompasses aspects of both ‘encoded one bead, one compound’ and the reductive approaches employed in chemistry. Biopanning is generally applied to display libraries, such as phage, bacterial, ribosome , RNA or on-bead display libraries, in which proteins are physically linked to their encoding sequence. This enables large libraries to be expressed and screened en masse for their ligand- binding properties. The library is screened by several rounds of biopanning, whereby the complexes are incubated with the desired target molecule, which is typically immobilized on a solid support. Subsequent washing removes the weakly binding proteins while retaining the desired proteins, which are then eluted for the next round of biopanning. Successively smaller numbers of displayed proteins are screened until ‘active’ proteins are isolated. The identity of the active protein borne on the display vehicle is established by sequencing the linked encoding sequence (DNA or RNA) of the carrier vehicle (phage, bacteria, ribosome or bead). Marcus D. Hughes, Zhan-Ren Zhang, Andrew J. Sutherland, Albert F. Santos and Anna V. Hine, Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins, Nucleic Acids Research 2005 33(3) http://nar.oupjournals.org/cgi/content/full/33/3/e32   Also referred to as panning.

carbohydrate chips: University scientists have described the first chip- based chemical strategy for rapidly screening carbohydrates for biologically useful activity. [Chemical method makes further investigation of carbohydrates possible, Univ. of Chicago Chronicle, 21 (3) April 11, 2002]   http://chronicle.uchicago.edu/020411/biochip.shtml  

carbohydrate microarrays: Stu Borman, Chemical and Engineering News, Dec. 16, 2002 lists as highlights of 2002  http://pubs.acs.org/cen/coverstory/8050/8050chemhighlights5.html with references to the literature on polysaccharide and glycoconjugate microarrays, monosaccharide chips, natural and synthetic oligosaccharide arrays, and synthetic oligosaccharides in microtiter plate format. 

cDNA phage display:  Display cloning: functional identification of natural product receptors using cDNA-phage display.  Sche PP, McKenzie KM, White JD, Austin DJ. Chem Biol. 1999 Oct;6(10):707- 716  

co-immunoprecipitation  Used to determine protein- protein interactions.  An antibody is used to precipitate a protein along with bound proteins. John Yates, “Mass spectrometry and the Age of the Proteome”  Journal Mass Spectrometry 33: 16, 1998

combinatorial biology: Involves genetic manipulation of bacteria and fungi that produce complex natural products. This technology includes construction of large libraries of recombinant microbes capable of generating novel organic molecules and engineering secondary metabolite biosynthetic pathways to modify valuable biologically active microbial metabolites. [ASB [Am Soc. Biomechanics] Newsletter, June 1998]   http://asb-biomech.org/newsletter/V11N1/guest.html    Wikipedia http://en.wikipedia.org/wiki/Combinatorial_biology   Related term: phage display

co-precipitation: Method to identify interacting proteins by using antibodies to bind to the protein if immunoprecipitated under non- denaturing using conditions … (allow any other proteins bound to the protein known to be involved in a process) to precipitate rather than be washed away.

depletion:  Method of sample preparation which removes high abundance proteins (not of interest) from the sample. Related term:  low- abundance proteins.

directed protein evolution: Proteomics Related term: phage display 

DNA shuffling: Genomic technologies Can be used to evolve proteins.

domain shuffling: Protein structure 

fluorescent proteins: Using fluorescence is turning into one of the premier technologies for drug discovery. To tap the full potential of these new and exciting opportunities, many challenges still need to be addressed: How to increase the stability of cell lines expressing fluorescent proteins; how to increase drug screening by using better disease models utilizing FP’s in whole organisms; how to develop better tools to enhance the high-throughput applications; and how to improve effectiveness while lowering costs.  Related terms: Labels Signaling & Detection  

Fluorescence Recovery After Photobleaching FRAP, Fluorescence Resonance Energy Transfer FRET: Labels Signaling & Detection

gene shuffling: Genomic technologies  Can be used to evolve proteins.

glycoarrays: Carbohydrates interact with proteins in many biological processes such as fertilization, virus infections and even tumor growth. Therefore, structural and functional aspects concerning the interplay of the glycome (the complete set of carbohydrate structures produced by a particular cell or tissue) and the proteome (set of proteins) are of great interest in biology and medicine. The aim of the present project is to develop carbohydrate arrays (glycoarrays) as innovative tools to map out the carbohydrate and protein partners in these highly specific interactions of the glycome. The project brings together a diverse set of novel technologies: from the generation of carbohydrate libraries (from natural sources, by chemical and enzymatic synthesis) and finding ways of linking the saccharides to a surface, to high throughput expression of carbohydrate binding proteins and the analysis of carbohydrate-protein binding by mass spectrometry, surface plasmon resonance and fluoresence measurements. UK Glycoarrays Consortium, 2009  http://www.glycoarrays.org.uk/ 

glycoprotein microarrays:  We employ carbohydrate and glycoprotein microarrays to analyze glycan- dependent gp120- protein interactions. In concert with new linking chemistries and synthetic methods, the carbohydrate arrays combine the advantages of microarray technology with the flexibility and precision afforded by organic synthesis. With these microarrays, we individually and competitively determined the binding profiles of five gp120 binding proteins, established the carbohydrate structural requirements for these interactions, and identified a potential strategy for HIV vaccine development. EW Adams et. al., Oligosaccharide and glycoprotein microarrays as tools in HIV glycobiology; glycan- dependent gp120/ protein interactions, Chem Biol. 11(6): 875- 881, June 2004   Related terms: oligosaccharide chips; Glycosciences glossary

intrabodies: Recent advances in antibody engineering have now allowed the genes encoding antibodies to be manipulated so that the antigen binding domain can be expressed intracellularly. The specific and high- affinity binding properties of antibodies, combined with their ability to be stably expressed in precise intracellular locations inside mammalian cells, has provided a powerful new family of molecules for gene therapy applications. These intracellular antibodies are termed 'intrabodies'. [Wayne A. Marasco, "Intrabodies: turning the humoral immune system outside in for intracellular immunization" Gene Therapy 4 (1): 11- 15, Jan. 1997

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

lambda phage: See under bacteriophage
molecular display: See under phage display
molecular evolution: Technologies overview

molecular motors: Protein based machines that are involved in or cause movement such as the rotary devices (flagellar motor and the F1 ATPase) or the devices whose movement is directed along cytoskeletal filaments (myosin, kinesin and dynein motor families). MeSH, 1999  
Wikipedia http://en.wikipedia.org/wiki/Molecular_motors

networks & pathways technologies: In the human body, all biological components—from individual genes to entire organs—work together to promote normal development and sustain health. This amazing feat of biological teamwork is made possible by an array of intricate and interconnected pathways that facilitate communication among genes, molecules, and cells. Limitations of proteomics technologies often force investigators to treat dynamic systems as either static or as binary options between static states. As with early photography, current approaches to proteomics involve long exposures that capture broadly defined "images" such as "normal vs. diseased", "the yeast interactome", or "the nuclear pore complex." We are largely blind to the dynamics of systems we know are not static but which must be treated as such for the time being because of inadequate tools. Transient interactions, rapid changes in protein activity or location, and post-translational modifications control critical regulatory steps in biology, yet they are like a bird flying through the frame of a carefully composed long exposure: invisible.  New strategies complementary to conventional proteomics are necessary to help us determine the rapid, dynamic changes that control physiology. The National Technology Centers for Networks and Pathways (TCNPs) create technologies to measure the dynamics of protein interactions, modifications, translocation, expression, and activity, and to do so with temporal, spatial, and quantitative resolution. The program is intended to bridge the quantitation and interaction aspects of proteomics, breaking out of the artificially static view of complex systems (Sheeley, Breen, and Old, J. Proteome Research (2005) 4,1114). The TCNP program was envisioned specifically to complement conventional proteomics programs at NIH, integrating proteomics with cell biology and biophysics, with an enhanced emphasis on novel approaches not substantially supported in other programs. National Technology Centers for Networks and Pathways,  NIH Common Fund http://commonfund.nih.gov/buildingblocks/technologycenters/overview.aspx 

oligosaccharide arrays: See glycochips, oligosaccharide microarrays

oligosaccharide microarrays: Studies on glycans are indispensable to define complex life systems and cell communities because all living organisms consist of diverse cells, which are covered with an abundance of heterogeneous carbohydrates. Although studies on glycans are extremely difficult because of the lack of basic technologies common to DNAs and proteins, a few new aspects of glycotechnologies have now become realized in the form of 'bio- chips', which include 'oligosaccharide arrays' or 'glyco- chips'. Recently, Fukui et al. developed oligosaccharide microarrays for glycomic analysis of extensive carbohydrate- binding proteins. How and why such glyco- engineering projects have been made in the contexts of both pure and applied sciences is described. J. Hirabayashi, Oligosaccharide microarrays for glycomics, Trends in Biotechnology 21 (4): 141-143, Apr. 2003    Related terms: glycochip, glycoprotein arrays 

peptide aptamers: Engineered protein molecules selected from combinatorial libraries, [used] to dissect the function of specific genes and alleles, and to trace genetic pathways. Roger Brent "Peptide aptamers" Molecular Sciences Institute, 1999  Broader term: aptamers 

peptide arrays:  Steve Fodor and colleagues at Affymax published several articles on these in the early 1990s.   Related terms protein arrays, protein chips, protein microarrays

Peptide Mass Fingerprinting PMF: A means of protein identification, using mass spectrometry

peptide sequencing: How is this different from protein sequencing (except that peptides are shorter than proteins)?

phage: A virus for which the natural host is a bacterial cell. DOE

Used as a vector for cloning segments of DNA. Schlindwein  Related terms: bacteriophage, phage display. 

phage display: Phage and Yeast Display of Antibodies and Recombinant ProteinsPhage and Yeast Display of Antibodies and Recombinant Proteins  May 5-6, 2014 • Boston, MA Program | Register | 

Use of genetically engineered phage to present peptides as segments of their native surface proteins. Peptide libraries may be produced by populations of phage with different gene sequences. IUPAC Combinatorial Chemistry  Broader term: display technologies  Related terms:  bacteriophage, biopanning, phage;  Labels, signaling & detection; Proteomics directed protein evolution  
photoaptamers:
Aptamers that incorporate a brominated deoxyuridine (BrdU) in place of the thymidine (T) normally found in DNA. A photoaptamer recognizes both the complex shape and charge distribution of its protein target and the presence of specific amino acid residues at specific sites. Related term: spiegelmer; Broader term: aptamers

PK/PD Novel constructs PK/PD of Novel ConstructsPK/PD of Novel Constructs  November 11-12, 2013 • Washington, DC Program | Register | 

prefractionation: Sample preparation method, capable of  being automated.

protein amplification: Potentially, the most revolutionary new technologies are those that impart the equivalent of PCR amplification on proteins. Two of these technologies, discussed in this report, are phage display and Profusion technology. In particular, Profusion has the capability of taking any pool of mRNA, translating it into protein/ mRNA fusion products, and following up any kind of selection protocol on the protein with further amplification. The company that is commercializing this technology, Phylos, is seeking to combine the method with other powerful screening techniques such as microarrays

protein arrays: Protein arrays are poised to become a central proteomics technology allowing for the global observation of biochemical activities on an unprecedented scale. Hundreds or thousands of proteins can be simultaneously screened for protein-protein, protein-nucleic acid, and small molecule interactions. The value of multiplexed protein measurement is being established in applications including: comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries, and clinical biomarker development. This technology holds great potential for basic molecular biology research, serum profiling, protein abundance determination, disease biomarker identification, immune and toxicological response profiling, and pharmaceutical target screeningRelated terms: antibody arrays, protein chips, protein microarrays Narrower terms: high- density protein arrays, protein- protein interaction chips, proteome chip

protein capture reagents:  The Common Fund’s Protein Capture Reagents program is developing new resources and tools to understand the critical role the multitude of cellular proteins play in normal development and health as well as in disease. These resources will support a wide-range of research and clinical applications that will enable the isolation and tracking of proteins of interest and permit their use as diagnostic biomarkers of disease onset and progression. NIH Common Fund http://commonfund.nih.gov/proteincapture/ 

protein delivery: Drug discovery & development

protein chips:  The protein chip is not going to replace certain discovery methods (such as 2D gel electrophoresis), which are very good at identifying novel proteins in a complex mixture. Perhaps the greatest limitation of methods based on electrophoresis is that they are relatively expensive to perform in terms of the cost per data point, and can be quite laborious. The trend, however, may continue toward reduced costs and ease of use. Another limitation of conventional proteomic methods is that they may not be versatile enough to rapidly gather biological information - changes in protein expression, protein- protein interactions, response to various conditions.

Ciphergen trademarked ProteinChip™ which is now owned by BioRad. Some chips can operate with both nucleic acids and proteins. Analogous to DNA chips, these are used for studying protein expression or protein- protein interactions.   Related terms: antibody arrays, carbohydrate chips, carbohydrate arrays, protein arrays, protein microarrays; Narrower terms: high- density protein microarrays, protein-protein interaction chips,  proteome chip

protein detection: New fluorescent stains (such as Sypro) have improved both the dynamic range of protein detection and protein quantification in 2D gels. "Current State of  Proteomic Technology"  CHI's Genome Link 3.1, 2001 http://www.chidb.com/newsarticles/issue3_1.ASP

protein engineering: A technique used to produce proteins with altered or novel amino acid sequences. The methods used are: 1. Transcription and translation systems from synthesized lengths of DNA or RNA with novel sequences. 2. Chemical modification of  'normal' proteins. 3. Solid-  state polypeptide synthesis to form proteins.  IUPAC Compendium

Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes. MeSH 2003

Procedures by which nonrandom single- site changes are introduced into structural genes (site- specific mutagenesis) in order to produce mutant genes which can be coupled to promoters that direct the synthesis of a specifically altered protein, which is then analyzed for structural and functional properties and then compared with the predicted and sought- after properties. The design of the protein may be assisted by computer graphic technology and other advanced molecular modeling techniques.  MeSH, 1989

The Protein Engineering Department combines biological, structural, chemical, and combinatorial approaches to explore protein functions and molecular interactions. … Specific achievements include: Improving existing proteins and enzymes to make them more effective — with higher affinity, longer lasting effects and/or greater selectivity  Determining three-dimensional structures of proteins and protein complexes  Finding new molecules with biological activity and exploring their potential as therapeutic agents or drug targets  Inventing new protein/peptide technologies  Applying chemical approaches to problems in drug discovery and biology. Genentech, Protein Engineering Science of Biotechnology http://www.gene.com/gene/research/biotechnology/proteinengineering.html 

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

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protein expression arrays: Expression glossary

protein expression profiling: Expression genes & proteins

protein inhibition: An alternative approach to [gene expression] downregulation, but in this case, the protein, not the gene, is the target. As with downregulation of gene expression, protein inhibition is a powerful target validation tool. The major approach to protein inhibition is based on phage libraries, which are used to select antibodies against targets of interest. 

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 localization:  There is an ever- increasing number of genes that have been sequenced but are of completely unknown function. The ability to determine the location of such gene products within the cell, either by the use of antibodies or by the production of chimeras with green fluorescent protein, is a vital step towards understanding what they do. This is one major reason why fluorescence microscopy is enjoying a revival. Protein Localization by Fluorescence Microscopy: A Practical Approach Edited by VICTORIA J. ALLAN, Oxford University Press, 2000 

Protein expression analysis can indicate what proteins are expressed, but it is also important to know where proteins are expressed, and where they go over time (as with secreted proteins). Accordingly, there is an increasing shift away from general protein expression analysis and toward mapping proteins’ distribution, relative abundance, tissue specificity, and movement. By tracking these parameters (in healthy versus diseased tissue and in control versus treated tissue), researchers can gain a greater understanding of these proteins’ functions and determine which are likely to be the best drug targets. Protein localization studies can be classified as being done at a tissue or subcellular level. "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink 15.2 http://www.chidb.com/newsarticles/issue15_2.asp  Narrower terms: subcellular localization, tissue specific localization; Related terms Cell biology:  subcellular fractionation; Gene definitions: gene localization; Omes & omics localizome

protein microarrays: These arrays can consist of proteins themselves (e.g., for studies of protein/ protein interactions or protein/ small- molecule binding) or of probes for capturing proteins (so that protein levels in a sample can be gauged). [CHI Microarrays report]      

In conjunction with high throughput expression and purification of recombinant proteins, we can prepare microarrays of functionally active proteins on glass slides. These arrays can then be used to identify protein- protein interactions, to identify the substrates of protein kinases, or to identify the targets of biologically active small molecules. [Harvard Center for Genomic Research, MacBeath Lab, Overview]  http://www.cgr.harvard.edu/macbeath/index.html

Protein microarrays will permit researchers to scan thousands of proteins in a variety of proteomic experiments, including differential expression, response to drugs, protein- protein interactions and identification of disease biomarkers. So far, they have proven to be very quantitative and, by virtue of their addressable arrays, much easier to compare results between experiments than 2D gels. Commercialization of protein arrays also promises rapid development toward real applications in clinical and point- of- care diagnostics, which would be impossible with more complex proteomic technologies that require electrophoresis or chromatography. One disadvantage of the microarray approach is that generally it is a "closed" system - you can only measure proteins for which you have a capturing agent (such as an antibody). 

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

Related terms: antibody microarrays, protein arrays, protein chips, protein profiling chips; Narrower terms:  electrospray- fabricated protein microarrays, functional protein microarrays, protein-protein interaction chips, proteome chip

protein profiling: Expression glossary 

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

protein purification: John Wagner's Logic of Molecular Approaches to Biological Problems (Cornell Univ. Graduate School of Medical Science, US ) has a section on the value of protein purification. http://www-users.med.cornell.edu/~jawagne/proteins_%26_purification.html

protein shuffling: We also constructed a computational method to determine the locations of crossovers that lead to functional hybrid proteins during in vitro recombination. Borrowing a concept from the schema theory of genetic algorithms, our approach assumes that crossovers resulting in functional proteins are those that least disrupt structural integrity. ... This method can be used to predict sites for protein shuffling and to screen sequence databases to determine optimal sets of starting sequences for in vitro evolution by recombination. Stephen L. Mayo, Computational Protein Design, Cal Tech, Howard Hughes Medical Institutehttp://www.hhmi.org/research/investigators/mayo.html 

proteolysis: Wikipedia http://en.wikipedia.org/wiki/Proteolysis  Research and diagnostic applications

proteolytic processing: Related terms proteolysis Broader term post- translational modification

proteome arrays, proteome chips: Microarrays & protein chips glossary 

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

quantitative proteomics: involves the identification and quantitation of protein components in various biological systems. Stable isotope labelling technology, by both metabolic and chemical methods, has been the most commonly used approach for global proteome-wide profiling. Recently, its capability has been extended from labelled pairs to multiple labels, allowing for the simultaneous quantification of multiplex samples. The ion intensity-based quantitative approach has progressively gained more popularity as mass spectrometry performance has improved significantly. Although some success has been reported, it remains difficult comprehensively to characterise the global proteome, due to its enormous complexity and dynamic range. The use of sub-proteome fractionation techniques permits a simplification of the proteome and provides a practical step towards the ultimate dissection of the entire proteome. Further development of the technology for targeting sub-proteomes on a functional basis - such as selecting proteins with differential expression profiles from mass spectrometric analyses, for further mass spectrometric sequencing in an intelligent manner--is expected in the near future.   Institute for Systems Biology, 2013https://www.systemsbiology.org/mass-spectrometry-based-quantitative-proteomic-profiling

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

recombinant proteins:  Proteins prepared by recombinant DNA technology.  MeSH, 1986  Related term: genetic recombination  

self-assembling biomolecular materials: Examples of self- assembly include protein folding, the formation of liposomes, and the alignment of liquid crystals. While this type of equilibrium self- assembly is the central focus of this report, it is important to emphasize that much biological assembly is also driven by energy sources such as adenosine triphosphate (ATP), which power biomotors  Biomolecular self- assembling materials, National Academy of Sciences 1996  http://www.nas.edu/bpa/reports/bmm/bmm.html#PBMM  Broader term: self-assembly

shotgun proteomics: Instrumentation aside, algorithms for matching mass spectra to proteins are at the heart of shotgun proteomics. How do these algorithms work, what can we expect of them and why is it so difficult to find protein modifications? Shotgun proteomics is a remarkably powerful technology for identifying proteins, whether individually or in samples as complex as cell lysates.  How do shotgun proteomics algorithms identify proteins? Edward M. Marcotte Nature Biotechnology 25, 755 - 757 (2007) doi:10.1038/nbt0707-755 http://www.nature.com/nbt/journal/v25/n7/full/nbt0707-755.html
Wikipedia http://en.wikipedia.org/wiki/Shotgun_proteomics

subcellular localization:  A variety of approaches—including tagging and fluorescence technologies, cellular isolation methods, gels, and mass spectrometry—are being used in these studies, which aim to track the location and/or movement of proteins or protein complexes in subcellular compartments.  "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink 15.2http://www.chidb.com/newsarticles/issue15_2.asp 

subcellular proteomics: See under subproteomics  

subcellular tissue-specific localization: A major methodology is an immunohistochemistry approach that uses antibodies (typically visualized via an enzyme- linked antibody assay) that specifically bind to proteins of interest. This method allows one not only to assess levels of a protein but also to localize the protein within cells in a tissue sample.  "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink http://www.chidb.com/newsarticles/issue15_2.asp 

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 2005http://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   

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

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

translation:  Sequences, DNA & beyond  Another approach to downregulating gene expression See also Genetic Manipulation & Disruption  RNAi; Pharmaceutical biology antisense; RNA  ribozymes

yeast display: See Biologics: antibody libraries

Bibliography
NFCR Center for Therapeutic Antibody Engineering Glossary, National Foundation for Cancer Research, Dana Farber Cancer Institute  http://research4.dfci.harvard.edu/nfcr-ctae/research/tech_glossary.php  
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.

 

Full-length cDNAs and ORF Full-length cDNAs and ORF clones are prerequisite for the construction of whole proteome arrays, for high throughput protein structural studies and for the rapid creation of protein fusion (GFP, TAP-tagged, etc.) for all proteins Joseph R. Ecker Plant Genome Research Program Grant: DBI9975718/0196098 "Global Expression Studies of the Arabidopsis Genome", The Salk Institute for Biological Studies protein purification: John Wagner's Logic of Molecular Approaches to Biological Problems (Cornell Univ. Graduate School of Medical Science, US ) has a section on the value of protein purification. http://www-users.med.cornell.edu/~jawagne/proteins_%26_purification.html

protein shuffling: We also constructed a computational method to determine the locations of crossovers that lead to functional hybrid proteins during in vitro recombination. Borrowing a concept from the schema theory of genetic algorithms, our approach assumes that crossovers resulting in functional proteins are those that least disrupt structural integrity. ... This method can be used to predict sites for protein shuffling and to screen sequence databases to determine optimal sets of starting sequences for in vitro evolution by recombination. Stephen L. Mayo, Computational Protein Design, Cal Tech, Howard Hughes Medical Institute http://www.hhmi.org/research/investigators/mayo.html Google = about 16 Sept. 8, 2003; about 30 Nov. 29, 2004; about 115 Nov. 10, 2006

proteolysis: Wikipedia http://en.wikipedia.org/wiki/Proteolysis  Research and diagnostic applications

proteolytic processing: Related terms proteolysis Broader term post- translational modification

proteome arrays: Full-length cDNAs and ORF clones are prerequisite for the construction of whole proteome arrays, for high throughput protein structural studies and for the rapid creation of protein fusion (GFP, TAP-tagged, etc.) for all proteins  [Joseph R. Ecker Plant Genome Research Program Grant: DBI9975718/0196098 "Global Expression Studies of the Arabidopsis Genome", The Salk Institute for Biological Studies http://signal.salk.edu/SSP.pdf.

Google = about 25 July 10, 2002; about 86  Sept. 16, 2003 Broader term: protein array

proteome chips:  To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. Global analysis of protein activities using proteome chips. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M., Science 293 (5537): 2101- 2105., Sept. 14, 2001 Epub 2001 Jul 26  Google = about 172 July 10, 2002; about 150 Sept. 16, 2003; about 555 Feb. 28,2005

proteome microarrays:   Broader terms: protein arrays, protein chips, protein microarrays; Narrower term: whole proteome microarrays

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

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 

recombinant proteins:  Proteins prepared by recombinant DNA technology.  MeSH, 1986  Related term: genetic recombination  

reverse chemical proteomics: Chemistry

self-assembling biomolecular materials: Examples of self- assembly include protein folding, the formation of liposomes, and the alignment of liquid crystals. While this type of equilibrium self- assembly is the central focus of this report, it is important to emphasize that much biological assembly is also driven by energy sources such as adenosine triphosphate (ATP), which power biomotors  Biomolecular self- assembling materials, National Academy of Sciences 1996  http://www.nas.edu/bpa/reports/bmm/bmm.html#PBMM  Broader term: self-assembly

structural biology: A healthy mind and body require the coordinated action of billions of tiny molecular workers called proteins. Our genes contain the DNA scripts for manufacturing these proteins. Some proteins build our cells and other proteins work to allow us to think, smell, eat and breathe. Proteins are indispensable molecules in our bodies, and each has a unique three-dimensional shape that is well suited for its particular job. And if the shape of even one protein happens to go awry, there can be major consequences for human health. Misshapen proteins, especially those that make up part of the cell surface or cell membranes, are the culprits behind many diseases, including cystic fibrosis, Alzheimer's disease and countless others.The Structural Biology Roadmap is a strategic effort to create a "picture" gallery of the molecular shapes of proteins in the body. This research investment will involve the development of rapid, efficient, and dependable methods to produce protein samples that scientists can use to determine the three-dimensional structure, or shape, of a protein. The new effort will catalyze what is currently a hit-or-miss process into a organized, coordinated, systematic and streamlined routine, helping researchers clarify the role of protein shape in health and disease. Structural biology, NIH Common Fund http://commonfund.nih.gov/structuralbiology/overview.aspx 

translation:  Sequences, DNA & beyond  Another approach to downregulating gene expression See also Genetic Manipulation & Disruption  RNAi; Pharmaceutical biology antisense; RNA  ribozymes

whole proteome microarrays: Google = about 2 Aug. 9, 2002; about  5 Sept. 16, 2003, about 6,980 March 3 2011  Related term: proteome chip

yeast display: See phage and yeast display; Biologics: antibody libraries

Bibliography
NFCR Center for Therapeutic Antibody Engineering Glossary, National Foundation for Cancer Research, Dana Farber Cancer Institute  http://research4.dfci.harvard.edu/nfcr-ctae/research/tech_glossary.php 
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.

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