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Proteomics categories & taxonomy

Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions?
Mary Chitty
Last revised January 09, 2020

Drug discovery & development term index:  Related glossaries include Protein informatics   Protein Technologies  ProteomicsProteinsProtein categoriesProtein Structures

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

bottom up proteomics: a common method to identify proteins and characterize their amino acid sequences and post-translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry.[1][2]  The major alternative workflow used in high-throughput proteomics is called top-down proteomics and does not use proteolytic digestion. Essentially, bottom-up proteomics is a means of determining the protein make-up of a given sample of cells, tissues, etc.[3]  Wikipedia acccessed 2018 Aug 28

computational proteomicsLarge- 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

differential proteomes: Mass spectrometry-based differential proteomics is a comprehensive analysis of protein expression that involves comparing distinct proteomes, such as cells, tissues or cell lines that are normal, diseased or treated. Mayo Clinic

differential proteomics: Mass spectrometry-based differential proteomics is a comprehensive analysis of protein expression that involves comparing distinct proteomes, such as cells, tissues or cell lines that are normal, diseased or treated. This type of analysis works best for defining differences between groups or treatments and for the initial "discovery" of potential biomarkers. Mayo Clinic Proteomics Core

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  Broader terms: subproteomes, subproteomics

functional proteomics:  constitutes an emerging research area in the proteomic field whose approaches are addressed towards two major targets: the elucidation of the biological function of unknown proteins and the definition of cellular mechanisms at the molecular level. METHODS: The identification of interacting proteins in stable complexes in vivo is essentially achieved by affinity-based procedures. The basic idea is to express the protein of interest with a suitable tag to be used as a bait to fish its specific partners out from a cellular extract. Individual components within the multi-protein complex can then be identified by mass spectrometric methodologies. RESULTS AND CONCLUSIONS: The association of an unknown protein with partners belonging to a specific protein complex involved in a particular mechanism is strongly suggestive of the biological function of the protein. Moreover, the identification of protein partners interacting with a given protein will lead to the description of cellular mechanisms at the molecular level. Functional proteomics. Monti M1, Orrù SPagnozzi DPucci P. . Clin Chim Acta. 2005 Jul 24;357(2):140-50.

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. 

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  

membrane proteomics:   Drug Targets

microproteomics: analysis of protein diversity in small samples.  Mass Spectrom Rev. 2008 Jul-Aug;27(4):316-30. doi: 10.1002/mas.20161. Microproteomics: analysis of protein diversity in small samples. Gutstein HBMorris JSAnnangudi SPSweedler JV.

molecular (and cellular) proteomics:  SCOPE OF THE JOURNAL Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights; Novel experimental and computational technologies; Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes; Pathway and network analyses of signaling that focus on the roles of post-translational modifications; Studies of proteome dynamics and quality controls, and their roles in disease; Studies of evolutionary processes effecting proteome dynamics, quality and regulation; Chemical proteomics, including mechanisms of drug action; Proteomics of the immune system and antigen presentation/recognition; Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease; Clinical and translational studies of human diseases; Metabolomics to understand functional connections between genes, proteins and phenotypes  Scope note Molecular and Cellular Proteomics  Related/equivalent term?: interaction proteomics

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  

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

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.

predictive proteomics: The search for predictive biomarkers of disease from high-throughput mass spectrometry (MS) data requires a complex analysis path. Preprocessing and machine-learning modules are pipelined, starting from raw spectra, to set up a predictive classifier based on a shortlist of candidate features. As a machine-learning problem, proteomic profiling on MS data needs caution like the microarray case. The risk of overfitting and of selection bias effects is pervasive: not only potential features easily outnumber samples by 103 times, but it is easy to neglect information-leakage effects during preprocessing from spectra to peaks. Machine learning methods for predictive proteomics, Annalissa Barla et. Al Briefings in Bioinformatics (2008) 9 (2): 119-128.

quantitative proteomics: Wikipedia

regulatory proteome: For a living cell to function in its environment, a large number of regulatory processes are needed, including regulation of cell proliferation, cell differentiation and cell death. The underlying mechanisms include regulation of gene expression, as well as, different post-translational modifications that control for example activity, stability, localization or degradation of the protein. An important class of regulatory proteins are transcription factors that determine when genes are switched on and off. About 1500 human transcription factors are known and these proteins are often differentially expressed in different parts of the human body.  Human Protein Atlas

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 

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"

shotgun proteomics: refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry.[1][2][3][4][5][6] The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing pattern of a shotgun. The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. Tandem mass spectrometry is then used to identify the peptides.Wikipedia accessed 2018 Aug 28

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

structural proteomics:
Sometimes referred to as structural genomics, this discipline involves determining the 3D structures of large numbers of proteins, ultimately accounting for an organism's entire proteome. It adds critical information in at least two points in the drug discovery pathway: (1) target identification, or selecting a pathway in which a drug might function, and (2) medicinal chemistry, or the actual design of compounds to modulate this pathway. A high-throughput, system wide means of determining gene function. It typically involves using high- throughput X-ray diffraction methods to determine the structure of proteins encoded by at least one member of each gene family in the genome. This approach is coupled with the use of bioinformatics as a tool in structural proteomics and computational modeling to determine structures of other proteins in the same family. Conversely, an important goal of structural proteomics is the creation of databases of structures. When asked to identify bottlenecks in the structural proteomics field, several academic and industry scientists pointed to the need for faster and more reliable protein production and purification strategies, rather than stronger beams at the X-ray crystallization step. 

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

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   

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

tissue proteomics:  The concept of tissues appeared more than 200 years ago, since textures and attendant differences were described within the whole organism components. Instrumental developments in optics and biochemistry subsequently paved the way to transition from classical to molecular histology in order to decipher the molecular contexts associated with physiological or pathological development or function of a tissue….Most recently, in the early 21(st) century, mass spectrometry (MS) has progressively become one of the most valuable tools to analyze biomolecular compounds. Currently, sampling methods, biochemical procedures, and MS instrumentations allow scientists to perform "in depth" analysis of the protein content of any type of tissue of interest. .. Tissue proteomics represents a veritable field of research and investment activity for modern biomarker discovery and development for the next decade. Tissue proteomics for the next decade? Towards a molecular dimension in histology. Longuespée R1Fléron MPottier CQuesada-Calvo FMeuwis MABaiwir DSmargiasso NMazzucchelli GDe Pauw-Gillet MCDelvenne PDe Pauw E.  OMICS. 2014 Sep;18(9):539-52. doi: 10.1089/omi.2014.0033. Epub 2014 Aug 8.

top down proteomics:   a method of protein identification that uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry analysis.[1][2] Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins.[3] The name is derived from the similar approach to DNA sequencing.[4] Proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance (Penning trap)[5], quadrupole ion trap (Paul trap) or Orbitrap mass spectrometer. Fragmentation for tandem mass spectrometry is accomplished by electron-capture dissociationor electron-transfer dissociation. Effective fractionation is critical for sample handling before mass-spectrometry-based proteomics. Proteome analysis routinely involves digesting intact proteins followed by inferred protein identification using mass spectrometry.[6] Top-down proteomics interrogates protein structure through measurement of an intact mass followed by direct ion dissociation in the gas phase.[7]  Wikipedia accessed 2018 Aug 28

toponomics:  a discipline in systems biology, molecular cell biology, and histology. [1][2]  It concerns the study of the toponome of organisms. The toponome is the spatial network code of proteins and other biomolecules in morphologically intact cells and tissues.[2][3] The terms toponome and toponomics were introduced by Walter Schubert in 2003[1] based on observations with imaging cycler microscopes (ICM). The term “toponome” is derived from the ancient Greek nouns “topos” (τόπος; place, position) and “nomos” (νόμος; law). Hence the term toponomics is descriptive term addressing the fact that the spatial network of biomolecules in cells follows topological rules enabling coordinated actions.[1] This spatial organization is directly revealed by imaging cycler microscopy with parameter- and dimension-unlimited functional resolution. Wikipedia accessed 2018 Jan 26

Proteomics resources
Nature “Post-Genomics Gateway”
UNI-PROT KnowledgeBase keywords   Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, 

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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