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Pharmaceutical Proteomics Glossary & taxonomy
Evolving Terminology for Emerging Technologies
 Suggestions? Revisions? Comments? Questions? 
 Mary Chitty
Last revised November 04, 2013
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Chemistry term index   Drug discovery term index   Informatics term index   Technologies term index    Biology term index   Site Map  Related glossaries include Proteomics categories  Applications: Functional genomicsMetabolic engineering,  
Informatics Protein Informatics   AlgorithmsBioinformatics  Drug discovery informatics 
Technologies:  Protein Technologies  Chromatography & electrophoresis,  Mass spectrometryNMR & x-ray crystallography
Biology: ExpressionProteinsProtein Structure 

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

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

biological atlas: Maps, genomic & genetic 
cell expression profiles: Cell biology 
cell mapping:
 Maps genomic & genetic Can determine subcellular locations of proteins.
cellular pathways: Metabolic engineering See under  metabolic engineering

cellular proteome: All of the proteins expressed in a cell. Google = about 948 Oct. 25, 2006

chemoproteomics: -Omes & -omics  Google = about 503 Oct. 25, 2006
clinical proteomics: Molecular Medicine
Google = about 435 Sept. 18, 2002; about 96,900 Oct. 25, 2006
combinatorial peptide libraries: Combinatorial libraries & synthesis

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

degradomics: -Omes & -omics  Google = about  59 Sept. 18, 2002' about 641 Oct. 25, 2006
designer proteins: Protein categories
Google = about  314 Sept. 18, 2002, about 10,900 Oct. 25, 2006
differential labeling: Labeling, signaling & detection 
Used for comparing the proteomes of different cell states. 
directed protein evolution: Google = about 902 Oct. 25, 2006

dissociator assays: A collective term for yeast- one hybrid, yeast- two hybrid or yeast- three hybrid assays.  Google = about 25 Oct. 25, 2006

domain: Protein structure
evolutionary genomics, evolutionary homology:  Phylogenomics

Expressed Protein Tags EPTs: Represent the collection of proteins which are present in a cell. Robert G. Urban "Proteomics: Making sense of the census" Current Drug Discovery, Aug. 2001  Related term: DNA EST expressed sequence tags 

FlexGene repository:  FLEX Full- Length Expression fragmentome:  -Omes & -omics
functional protein microarrays: Microarrays categories
functional proteomics: Proteomics categories
Google = about 3,160 Sept. 18, 2002; about 152,000 Oct. 25, 2006
glycosylation: Proteins
high- throughput proteomics: Proteomics categories 

homointeraction: A lot of proteins interact with themselves. [Dr. Jong Paik, Bioinformatics/ Proteomics, Dunn Human Nutrition Unit, Medical Research Council,  UK, 2001]

Human Plasma Proteome: See under Human Proteome
Human Proteome: See Plasma Proteome  

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

Human Proteome draft  
Human Proteome Initiative now Chordata Protein Annotation Program  http://www.uniprot. org/program/Chordata  one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, we are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artefacts and protein products derived from erroneous gene model predictions are also revisited.

immunoproteomics: -Omes & -Omics
interaction proteomics: Proteomics categories
Google = about  73 Sept. 18, 2002; about 403 Feb. 17, 2005; about 697 Oct. 25, 2006
interactome, interactomics: Omes & omics
localization: SEE protein localization Protein technologies
localizome: Omes & omics
localizome mapping: Maps, genomic & genetic

next-generation targeted proteomics: SRM [Selected Reaction Monitoring] is the most mature mass spectrometry–based technology for targeted proteome analysis, but new methodologies that obviate the need for laborious SRM assay optimization are on the horizon. With an approach called SWATH, complex mass spectra generated by data-independent acquisition (in which peptides are selected for fragmentation without regard to signal intensity) are queried for the presence of specific peptides using libraries of qualified peptide fragment spectra. With another new approach called parallel reaction monitoring, all transitions are monitored in parallel in a single analysis. Allison Doerr, Mass Spectrometry based targeted proteomics, Nature Methods  10, 23 (2013) doi:10.1038/nmeth.2286 Published online 27 Dec 2012 journal/v10/n1/full/nmeth. 2286.html
NHLBI Proteomics :
NHLBI launched a new proteomics program on August 15, 2010, by awarding contracts totaling $83.5 million to seven institutions across the United States. The new network consists of Boston University, Johns Hopkins University, Massachusetts General Hospital, Stanford University, the University of California-Los Angeles, the University of Texas Health Sciences Center at San Antonio, and the University of Texas Medical Branch at Galveston. 

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

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

pharmacoproteomics:   Pharmacogenomics Google = about 195 Sept. 18, 2002, about 488 July 14, 2004; about 12,200 Oct. 25, 2006
phosphorylation: Proteins

plasma proteome:
During 2003-2005, the PPP prepared and distributed reference specimens of human serum and plasma to 55 participating laboratories worldwide, stimulated access to emerging technologies, and generated substantial datasets and integrated databases for proteins detectable and identifiable in human serum and plasma. Experimental protocols used combinations of depletion, fractionation, mass spectrometry, and immunoassay methods linked via search engines and annotation groups to gene and protein databases. We created a new human plasma proteome database and have developed recommendations for use in future studies with plasma and serum. ..The findings from the collaborative project and from lab-specific ancillary projects are published in a special issue of Proteomics, "Exploring the Human Plasma Proteome", August 2005 HUPO Plasma Proteome Project 

Comprehensive, systematic characterization of the plasma proteome in healthy and diseased states greatly facilitates the development of biosignatures for early disease detection, clinical diagnosis, and therapy. However, blood plasma is the most complex human-derived proteome containing other tissue proteome subsets as well as a wide dynamic range of protein concentrations. 

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

post-translational modifications: Post-Translational Modifications  March 24-25, 2014 • Biotherapeutics Analytical Summit Baltimore, MD Program | Register | Download Brochure

Proteins once synthesized on the ribosomes, are subject to a multitude of modification steps. They are cleaved (thus eliminating signal sequences, transit or pro- peptides and initiator methionines); many simple chemical groups can be attached to them … as well as some more complex molecules, such as sugars and lipes. Finally they can be internally or externally cross- linked. More than a hundred different types of post- translational modifications are currently known (Aug. 1999) and many more are yet to be discovered. The complexity due to all these modifications is compounded by the high level of diversity that alternative splicing can produce at the level of sequence. Thus the number of different protein molecules expressed by the human genome is probably closer to a million than to the hundred thousand generally considered by genome scientists. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Amos Bairoch* Rolf Apweiler  Nucleic Acids Research 28 (1): 45-48  

Post-translational modification is a point of concern in the development of strategies for proteomics. Because these modifications cannot be inferred directly from gene sequence, they generally can only be characterized directly. This raises issues about sequence coverage and stoichiometry of modifications that are not presented by proteomics problems focused on protein identification. In particular, the complexity and diversity of glycosylation events significantly complicates the linkage between genetic sequence and mature, active proteins. Because glycosylation is mediated by a wide range of factors, discovery- based analytical tools that can survey the complexities of glycosylation on a system-wide basis may have significant biological impact. NCRR National Center for Research Resources, NIH, Integrated Biomedical Technology Research Resources for Proteomics and Glycomics,  RELEASE DATE: July 22, 2002 PA NUMBER: PA-02-132  Narrower terms: biotinylation, glycosylation, pegylation, phosphorylation, polyadenylation, prenylation, protein isoprenylation; Related terms: post- translational protein processing, proteolytic processing, ubiquitination; In silico & molecular modeling: post- translational modification prediction

post-translational protein processing: Any of various enzymically catalyzed post- translational modifications of peptides or proteins in the cell of origin. These modifications include carboxylation, hydroxylation, acetylation, glycosylation, methylation, phosphorylation, oxidation- reduction, degradation and lysis, peptide bond formation, and changes in molecular weight and electrophoretic motility. MeSH, 1983  Related terms: post- translational modifications; 

protein- carbohydrate interactions: The overarching goal of the [Consortium for Functional Glycomics] program is to: Define paradigms by which protein-carbohydrate interactions mediate cell communication. Consortium for Functional Glycomics, funded by NIGMS, US

protein arrays, protein chips: Microarrays & protein chips Google = about  2,450 Sept. 18, 2002; about 7.450 July 14, 2004; about 113,000 Nov 10, 2006 

protein complexes:    Related terms: complexome: -Omes & -omics; Metabolic engineering

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

protein- protein interactions: Drug & disease targets 
Protein interaction databases Databases & software directory.

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

protein-RNA interactions: Can be detected by the yeast three- hybrid assay. [John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College] 

Involved in gene expression and protein synthesis Related terms: interaction proteomics; Omes & omics  riboproteomics; Cell biology  ribosome,  

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

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

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

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

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


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

proteomic diversity: Alternative RNA splicing generates extreme proteomic diversity in the mammalian nervous system, where hundreds of thousands of distinct proteins are generated from approximately 30,000 genes. These protein counterparts play important roles in learning and memory, cell communication, and neural development. Paula Grabowski, Dept. of Biological Sciences, Univ. of Pittsburgh, US, 2001  Related term: RNA alternative RNA splicing

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

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

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

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

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

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

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

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

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?) 

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

Harvard Institute of Proteomics:

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]  

riboproteomics: RNA 

shotgun proteomics: Proteomics categories 
single cell proteomics: Ultrasensitivity 

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

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

targeted proteomics: The goal of a targeted proteomics experiment is to monitor a select few proteins of interest with high sensitivity, reproducibility and quantitative accuracy.  Mass spectrometry–based targeted proteomics, Allison Doerr, Nature Methods 10,23 (2013) doi:10.1038/nmeth.2286 Published online 27 dec 2013 journal/v10/n1/full/nmeth. 2286.html

toxicoproteomics: Pharmacogenomics  

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

yeast localizome: See under Proteins protein localization

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

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

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.   Related term  protein- RNA interactions.

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

A system first developed in 1989 (by Stan Fields and colleagues) to identify proteins (and their genes) that interact with known proteins.   Related terms: dissociator assays, reverse two hybrid, two hybrid system techniques, bait, prey

Folding@home glossary, Stanford Univ. Tug Sezen, Vijay Pande, 2002, 200+ definitions
National Academy of Sciences, Defining the Mandate of Proteomics in the Post- Genomics Era,  2002
National Academy of Sciences, Technology, Science and Economic Policy Board, Workshop on Exploring Patent and Licensing  Policy for Proteomics, June 2004  
Nature, “Post-Genomics Gateway”
Nature Proteomics, Mar 2003 
Nature, "Proteomics in action"
Nature Reviews Proteomics, 2005 
UNI-PROT KnowledgeBase keywords,  Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, PIR Protein Information Resource, 2007 

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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