Proteomics: The systematic study of the complete complement of proteins (PROTEOME) of organisms.Proteome: The protein complement of an organism coded for by its genome.Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Tandem Mass Spectrometry: A mass spectrometry technique using two (MS/MS) or more mass analyzers. With two in tandem, the precursor ions are mass-selected by a first mass analyzer, and focused into a collision region where they are then fragmented into product ions which are then characterized by a second mass analyzer. A variety of techniques are used to separate the compounds, ionize them, and introduce them to the first mass analyzer. For example, for in GC-MS/MS, GAS CHROMATOGRAPHY-MASS SPECTROMETRY is involved in separating relatively small compounds by GAS CHROMATOGRAPHY prior to injecting them into an ionization chamber for the mass selection.Electrophoresis, Gel, Two-Dimensional: Electrophoresis in which a second perpendicular electrophoretic transport is performed on the separate components resulting from the first electrophoresis. This technique is usually performed on polyacrylamide gels.Chromatography, Liquid: Chromatographic techniques in which the mobile phase is a liquid.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Isotope Labeling: Techniques for labeling a substance with a stable or radioactive isotope. It is not used for articles involving labeled substances unless the methods of labeling are substantively discussed. Tracers that may be labeled include chemical substances, cells, or microorganisms.Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization: A mass spectrometric technique that is used for the analysis of large biomolecules. Analyte molecules are embedded in an excess matrix of small organic molecules that show a high resonant absorption at the laser wavelength used. The matrix absorbs the laser energy, thus inducing a soft disintegration of the sample-matrix mixture into free (gas phase) matrix and analyte molecules and molecular ions. In general, only molecular ions of the analyte molecules are produced, and almost no fragmentation occurs. This makes the method well suited for molecular weight determinations and mixture analysis.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Protein Array Analysis: Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Peptide Mapping: Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Biological Markers: Measurable and quantifiable biological parameters (e.g., specific enzyme concentration, specific hormone concentration, specific gene phenotype distribution in a population, presence of biological substances) which serve as indices for health- and physiology-related assessments, such as disease risk, psychiatric disorders, environmental exposure and its effects, disease diagnosis, metabolic processes, substance abuse, pregnancy, cell line development, epidemiologic studies, etc.Spectrometry, Mass, Electrospray Ionization: A mass spectrometry technique used for analysis of nonvolatile compounds such as proteins and macromolecules. The technique involves preparing electrically charged droplets from analyte molecules dissolved in solvent. The electrically charged droplets enter a vacuum chamber where the solvent is evaporated. Evaporation of solvent reduces the droplet size, thereby increasing the coulombic repulsion within the droplet. As the charged droplets get smaller, the excess charge within them causes them to disintegrate and release analyte molecules. The volatilized analyte molecules are then analyzed by mass spectrometry.Two-Dimensional Difference Gel Electrophoresis: Methods of comparing two or more samples on the same two-dimensional gel electrophoresis gel.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Metabolomics: The systematic identification and quantitation of all the metabolic products of a cell, tissue, organ, or organism under varying conditions. The METABOLOME of a cell or organism is a dynamic collection of metabolites which represent its net response to current conditions.Chemical Fractionation: Separation of a mixture in successive stages, each stage removing from the mixture some proportion of one of the substances, for example by differential solubility in water-solvent mixtures. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Systems Biology: Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Blood Proteins: Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.Oxygen Isotopes: Stable oxygen atoms that have the same atomic number as the element oxygen, but differ in atomic weight. O-17 and 18 are stable oxygen isotopes.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Protein Interaction Maps: Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.Search Engine: Software used to locate data or information stored in machine-readable form locally or at a distance such as an INTERNET site.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Complex Mixtures: Mixtures of many components in inexact proportions, usually natural, such as PLANT EXTRACTS; VENOMS; and MANURE. These are distinguished from DRUG COMBINATIONS which have only a few components in definite proportions.Bacterial Proteins: Proteins found in any species of bacterium.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.

*  Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

... based proteomics measures peptides derived from proteins by proteolytic cleavage. Before performing the analysis by matrix- ... Mass spectrometry (MS)-based proteomics measures peptides derived from proteins by proteolytic cleavage. Before performing the ... Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. ...

*  Comparative proteomics analysis of caspase-9-protein complexes in untreated and cytochrome c/dATP stimulated lysates of NSCLC...

We used a proteomics approach to identify proteins in caspase-9-protein complexes in extracts derived from NSCLC cells with(out ... Comparative proteomics analysis of caspase-9-protein complexes in untreated and cytochrome c/dATP stimulated lysates of NSCLC ...

*  BibMe: Generate Clinical Proteomics preface / foreword citations for your bibliography

If required by your instructor, you can add annotations to your citations. Just select Add Annotation while finalizing your citation. You can always edit a citation as well. ...

*  Quantitative Proteomic Study of Human Lung Squamous Carcinoma and Normal Bronchial Epithelial Acquired by Laser Capture...

Proteomics provides a new opportunity to reveal the carcinogenic mechanism of HLSC. The comparative proteomics compares the ... The quantitative proteomics is one of the emerging fields for tumor proteomics study; isotope labeling relative and absolute ... Proteomics has become the frontier era of the postgenomic; the new methods and achievements are emerging in large number. ... iTRAQ quantitative proteomics can overcome that deficiencies (such as identified membrane proteins) and increase the number and ...

*  BibMe: Generate Clinical Proteomics advertisement citations for your bibliography

The month, day, and year a content piece was published electronically (as opposed to in print). Depending on the webpage, it may or may not be shown ...

*  Sensors | Free Full-Text | Identification of Cell-Surface Molecular Interactions under Living Conditions by Using the Enzyme...

... antibody array system and mass spectrometry-based proteomics approaches are available. Spatio- temporally-regulated interaction ...

*  Overview - Proteomics Core - Mayo Clinic Research

Through the Proteomics Core, investigators at Mayo Clinic and elsewhere have access to a broad range of proteomics services, ... The director of the Proteomics Core is Daniel J. McCormick, Ph.D. Dr. McCormick and his staff have extensive expertise in ... Proteomics involves the analysis and identification of protein structure and function. ... the core offers services and conducts research in the areas of mass spectrometry-based differential proteomics, peptide ...

*  Caprion Proteomics Inc. Company Profile

Caprion Proteomics is the leading provider of proteomics based services to the pharmaceutical and biotech industries. Caprion ... Caprion Proteomics Inc. company data, news, contact details and stock information. ... Informed-Proteomics: open-source software package for top-down proteomics. Informed-Proteomics, a software suite for top-down ... Caprion Proteomics Inc.. Caprion Proteomics is the leading provider of proteomics based services to the pharmaceutical and ...

*  Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.

... ... Proteomic analyses of different subcellular compartments, so-called organellar proteomics, facilitate the understanding of ...

*  NEWSBRIEF: Thermo Finnigan, MDS Proteomics Will Jointly Develop FTMS Proteomics System | GenomeWeb

May 9-Equipment manufacturer Thermo Finnigan and MDS Proteomics said today that they plan to work together to adapt mass ... NEWSBRIEF: Thermo Finnigan, MDS Proteomics Will Jointly Develop FTMS Proteomics System. May 09, 2002 ... Home » NEWSBRIEF: Thermo Finnigan, MDS Proteomics Will Jointly Develop FTMS Proteomics System ... NEW YORK, May 9-Equipment manufacturer Thermo Finnigan and MDS Proteomics said today that they plan to work together to adapt ...

*  total cell protein vs membrane protein - Protein and Proteomics - BioForum

... posted in Protein and Proteomics: I used MPER(pierce) for total cell proteins and RIPA buffer for membrane protein extractions ...

*  COST | Farm Animal Proteomics

The COST Action will form a network of the leading European scientists who are focused on farm animal proteomics; this network ... Farm Animal Proteomics Descriptions are provided by the Actions directly via e-COST. ...

*  Serum Proteomics Analysis for Sepsis - Full Text View -

Serum Proteomics Analysis for Sepsis. The recruitment status of this study is unknown. The completion date has passed and the ... Serum proteomics is a very useful tool to identify various disease. The purpose of the present study was to find differential ... Serum Proteomics Analysis for Dynamic Changes of Differential Proteins in Sepsis Patient With iTRAQ Labeling and LC-MS/MS. ..."Sepsis"&rank=10

*  An overview of the basics of proteomics - Education -

Deoxyribonucleic Acid to Ribonucleic Acid Ribonucleic Acid to Protein Proteome Handling in Classical and Functional Proteomics ... In this free chapter from Industrial Proteomics Applications for Biotechnology and Pharmaceuticals Daniel Figeys gives a basic ... Classical Proteomics *Gel-Free Analysis: An Alternative Differential Display. *Fourier Transofrm Mass Spectrometery for Gel- ... This book covers both basic elements and the state-of-the-art in applications of proteomics. The first section gives an ...

*  PPT - Proteomics PowerPoint Presentation - ID:710034

Proteomics. Proteomics directly detects expression of proteins. . Proteome research permits the discovery of new protein ... Introduction to Proteomics -What is proteomics?. proteomics - a newly emerging field of life science research that uses high ... Proteomics. Proteomics. Proteomics directly detects expression of proteins. . Proteome research permits the discovery of new ... Proteomics and annotation -Definition of proteomics. study of all the proteins in an organismderived from genomics all the dna ...

*  Playing for keeps - Protein and Proteomics - BioForum

... posted in Protein and Proteomics: Hi, I did SDS PAGE on cell lysate ( lysed with 1X sample buffer) yesterday. I still have some ...

*  Vamsi Mootha: Taking an inventory of mitochondria | JEM

I heard Matthias Mann give a talk about tandem mass spectrometry-based proteomics. ...

*  BibMe: Generate Clinical Proteomics photograph citations for your bibliography

Generate Clinical Proteomics citations for Photographs. Type. Personal photograph Not a personal photograph ...

*  Modulating protein function through reversible oxidation: Redox-mediated processes in plants revealed through proteomics -...

Redox-mediated processes in plants revealed through proteomics. Proteomics, 13: 579-596. doi: 10.1002/pmic.201200270 ... Redox proteomics studies on reversible oxidative and nitrosative protein modifications in plants. ... Modulating protein function through reversible oxidation: Redox-mediated processes in plants revealed through proteomics. ...

*  Frontiers | Using 7 cm immobilized pH gradient strips to determine levels of clinically relevant proteins in wheat grain...

The comparison with recent quantitative study suggested that gel-based and gel-free proteomics approaches are complementary for ... The comparison with recent quantitative study suggested that gel-based and gel-free proteomics approaches are complementary for ... The aim of the work was to test relatively simple proteomics approach based on phenol extraction, two-dimensional ... The aim of the work was to test relatively simple proteomics approach based on phenol extraction, two-dimensional ...

*  Hochschulschriften / Development of a quantitative proteomics method to study the...

Development of a quantitative proteomics method to study the adaption of fungi to extreme environments / Sandra Stranzinger. ... Development of a quantitative proteomics method to study the adaption of fungi to extreme environments [3.21 mb]. ... Development of a quantitative proteomics method to study the adaption of fungi to extreme environments / Sandra Stranzinger ...

*  News in Proteomics Research: Proteomic analysis of patients with cerebral and uncomplicated malaria

For a more uplifting tail, I suggest this nice recent paper from Bertin et al.,. In this work, these authors take a proteomic run at some patient sera with non-complicated (bad) and cerebral (really really really bad) Plasmodium falciparum (the species that generally kills you the first go 'round) malaria. They used label free quan and an Orbitrap Velos and some clever bioinformatic tricks (compound databases with lots of the Var sequences) and sweet downstream statistics to try and find some differences ...

*  Danny Hillis: Understanding cancer through proteomics | TED Talk

As Hillis explains it, genomics shows us a list of the ingredients of the body -- while proteomics shows us what those ... proteomics, the study of proteins in the body. ... proteomics, the study of proteins in the body. As Hillis ... explains it, genomics shows us a list of the ingredients of the body - while proteomics shows us what those ingredients produce ...

*  Testis whole cell lysate, normal tissue (ab29289)|Abcam

Proteomics tools. Agonists, activators, antagonists and inhibitors. Lysates. Multiplex miRNA assays. By research area. Cancer. ...

*  Proteomics Takes a Leap | Science | AAAS

Proteomics Takes a Leap. By Robert F. Service. Jul. 26, 2001 , 7:00 PM. ...

Proteomics Standards Initiative: The Proteomics Standards Initiative (PSI) is a working group of Human Proteome Organization. It aims to define data standards for proteomics in order to facilitate data comparison, exchange and verification.Plant Proteome Database: The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each protein in plants.Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ.Atomic mass: right |thumb|200px|Stylized [[lithium-7 atom: 3 protons, 4 neutrons, & 3 electrons (total electrons are ~1/4300th of the mass of the nucleus). It has a mass of 7.Tandem mass spectrometry: 300 px|right|thumb|A [[Quadrupole mass analyzer|quadrupole time-of-flight hybrid tandem mass spectrometer.]]Two-dimensional gel electrophoresisHuman Proteinpedia: Human Proteinpedia is a portal for sharing and integration of human proteomic data,.Kandasamy et al.Isotope-coded affinity tag: An Isotope-coded affinity tag (ICAT) is an isotopic labeling method used for quantitative proteomics by mass spectrometry that uses chemical labeling reagents. "Rapid quantitative analysis of proteins or protein function in complex mixtures," Rudolf Hans Aebersold et al.Soft laser desorption: Soft laser desorption is laser desorption of large molecules that results in ionization without fragmentation. "Soft" in the context of ion formation means forming ions without breaking chemical bonds.Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Peptide microarray: A peptide microarray (also commonly known as peptide chip or peptide epitope microarray) is a collection of peptides displayed on a solid surface, usually a glass or plastic chip. Peptide chips are used by scientists in biology, medicine and pharmacology to study binding properties and functionality and kinetics of protein-protein interactions in general.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.SEA Native Peptide LigationMac OS X Server 1.0Protein subcellular localization prediction: Protein subcellular localization prediction (or just protein localization prediction) involves the computational prediction of where a protein resides in a cell.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Generalizability theory: Generalizability theory, or G Theory, is a statistical framework for conceptualizing, investigating, and designing reliable observations. It is used to determine the reliability (i.Coles PhillipsOntario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.KIAA0895L: Uncharacterized protein KIAA0895-like also known as LOC653319, is a protein that in humans is encoded by the KIAA0895L gene.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?Biomarkers of aging: Biomarkers of aging are biomarkers that better predict functional capacity at a later age than chronological age. Stated another way, biomarkers of aging would give the true "biological age", which may be different from the chronological age.Electrospray ionizationDifference gel electrophoresis: Difference gel electrophoresis (DIGE) is a form of gel electrophoresis where up to three different protein samples can be labeled with size-matched, charge-matched spectrally resolvable fluorescent dyes (for example Cy3, Cy5, Cy2) prior to two-dimensional electrophoresis.Unlü M, Morgan ME, Minden JS.Protein–protein interactionMetabolomics: Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles.List of systems biology conferences: Systems biology is a biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences.Flux (metabolism): Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway.SciDBBlood proteins: Plasma proteins, also termed serum proteins or blood proteins, are proteins present in blood plasma. They serve many different functions, including transport of lipids, hormones, vitamins and minerals in the circulatory system and the regulation of acellular activity and functioning of the immune system.THC-O-phosphateImmersive technologyArk (search engine): Ark is a personal search engine that uses filters such as hometown, current city, high school, college, gender, relationship status, employee, and interests, to search for new people, old classmates, old friends or acquaintances, and new business contacts. Features include managing users' inboxes from their mobile devices, and syncing data from their Yahoo, Aol, Gmail or Google Apps email accounts, while also finding information about whom they are communicating with.Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.Cancer biomarkers: A cancer biomarker refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker may be a molecule secreted by a tumor or a specific response of the body to the presence of cancer.Potash: Potash is any of various mined and manufactured salts that contain potassium in water-soluble form.Potash, USGS 2008 Minerals Yearbook The name derives from "pot ash", which refers to plant ashes soaked in water in a pot, the primary means of manufacturing the product before the industrial era.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Matrix model: == Mathematics and physics ==

(1/9620) Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach.

BACKGROUND: Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include the development of classification systems capable of distinguishing between subfamilies within a structurally and functionally diverse superfamily. This would be helpful in elucidating sequence-structure-function relationships of proteins. RESULTS: Here, we present a method to diagnose sequences into subfamilies by employing hidden Markov models (HMMs) to find windows of residues that are distinct among subfamilies (called signatures). The method starts with a multiple sequence alignment (MSA) of the subfamily. Then, we build a HMM database representing all sliding windows of the MSA of a fixed size. Finally, we construct a HMM histogram of the matches of each sliding window in the entire superfamily. To illustrate the efficacy of the method, we have applied the analysis to find subfamily signatures in two well-studied superfamilies: the cadherin and the EF-hand protein superfamilies. As a corollary, the HMM histograms of the analyzed subfamilies revealed information about their Ca2+ binding sites and loops. CONCLUSIONS: The method is used to create HMM databases to diagnose subfamilies of protein superfamilies that complement broad profile and motif databases such as BLOCKS, PROSITE, Pfam, SMART, PRINTS and InterPro.  (+info)

(2/9620) Protein interactions: two methods for assessment of the reliability of high throughput observations.

High throughput methods for detecting protein interactions require assessment of their accuracy. We present two forms of computational assessment. The first method is the expression profile reliability (EPR) index. The EPR index estimates the biologically relevant fraction of protein interactions detected in a high throughput screen. It does so by comparing the RNA expression profiles for the proteins whose interactions are found in the screen with expression profiles for known interacting and non-interacting pairs of proteins. The second form of assessment is the paralogous verification method (PVM). This method judges an interaction likely if the putatively interacting pair has paralogs that also interact. In contrast to the EPR index, which evaluates datasets of interactions, PVM scores individual interactions. On a test set, PVM identifies correctly 40% of true interactions with a false positive rate of approximately 1%. EPR and PVM were applied to the Database of Interacting Proteins (DIP), a large and diverse collection of protein-protein interactions that contains over 8000 Saccharomyces cerevisiae pairwise protein interactions. Using these two methods, we estimate that approximately 50% of them are reliable, and with the aid of PVM we identify confidently 3003 of them. Web servers for both the PVM and EPR methods are available on the DIP website (  (+info)

(3/9620) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

Quantitative proteomics has traditionally been performed by two-dimensional gel electrophoresis, but recently, mass spectrometric methods based on stable isotope quantitation have shown great promise for the simultaneous and automated identification and quantitation of complex protein mixtures. Here we describe a method, termed SILAC, for stable isotope labeling by amino acids in cell culture, for the in vivo incorporation of specific amino acids into all mammalian proteins. Mammalian cell lines are grown in media lacking a standard essential amino acid but supplemented with a non-radioactive, isotopically labeled form of that amino acid, in this case deuterated leucine (Leu-d3). We find that growth of cells maintained in these media is no different from growth in normal media as evidenced by cell morphology, doubling time, and ability to differentiate. Complete incorporation of Leu-d3 occurred after five doublings in the cell lines and proteins studied. Protein populations from experimental and control samples are mixed directly after harvesting, and mass spectrometric identification is straightforward as every leucine-containing peptide incorporates either all normal leucine or all Leu-d3. We have applied this technique to the relative quantitation of changes in protein expression during the process of muscle cell differentiation. Proteins that were found to be up-regulated during this process include glyceraldehyde-3-phosphate dehydrogenase, fibronectin, and pyruvate kinase M2. SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system.  (+info)

(4/9620) Biophysical characterization of proteins in the post-genomic era of proteomics.

Proteomics focuses on the high throughput study of the expression, structure, interactions, and, to some extent, function of large numbers of proteins. A true understanding of the functioning of a living cell also requires a quantitative description of the stoichiometry, kinetics, and energetics of each protein complex in a cellular pathway. Classical molecular biophysical studies contribute to understanding of these detailed properties of proteins on a smaller scale than does proteomics in that individual proteins are usually studied. This perspective article deals with the role of biophysical methods in the study of proteins in the proteomic era. Several important physical biochemical methods are discussed briefly and critiqued from the standpoint of information content and data acquisition. The focus is on conformational changes and macromolecular assembly, the utility of dynamic and static structural data, and the necessity to combine experimental approaches to obtain a full functional description. The conclusions are that biophysical information on proteins is a useful adjunct to "standard" proteomic methods, that data can be obtained by high throughput technology in some instances, but that hypothesis-driven experimentation may frequently be required.  (+info)

(5/9620) A proteomic analysis of human cilia: identification of novel components.

Cilia play an essential role in protecting the respiratory tract by providing the force necessary for mucociliary clearance. Although the major structural components of human cilia have been described, a complete understanding of cilia function and regulation will require identification and characterization of all ciliary components. Estimates from studies of Chlamydomonas flagella predict that an axoneme contains > or = 250 proteins. To identify all the components of human cilia, we have begun a comprehensive proteomic analysis of isolated ciliary axonemes. Analysis by two-dimensional (2-D) PAGE resulted in a highly reproducible 2-D map consisting of over 240 well resolved components. Individual protein spots were digested with trypsin and sequenced using liquid chromatography/tandem mass spectrometry (LC/MS/MS). Peptide matches were obtained to 38 potential ciliary proteins by this approach. To identify ciliary components not resolved by 2-D PAGE, axonemal proteins were separated on a one-dimensional gel. The gel lane was divided into 45 individual slices, each of which was analyzed by LC/MS/MS. This experiment resulted in peptide matches to an additional 110 proteins. In a third approach, preparations of isolated axonemes were digested with Lys-C, and the resulting peptides were analyzed directly by LC/MS/MS or by multidimensional LC/MS/MS, leading to the identification of a further 66 proteins. Each of the four approaches resulted in the identification of a subset of the proteins present. In total, sequence data were obtained on over 1400 peptides, and over 200 potential axonemal proteins were identified. Peptide matches were also obtained to over 200 human expressed sequence tags. As an approach to validate the mass spectrometry results, additional studies examined the expression of several identified proteins (annexin I, sperm protein Sp17, retinitis pigmentosa protein RP1) in cilia or ciliated cells. These studies represent the first proteomic analysis of the human ciliary axoneme and have identified many potentially novel components of this complex organelle.  (+info)

(6/9620) A proteomics approach for the identification of DNA binding activities observed in the electrophoretic mobility shift assay.

Transcription factors lie at the center of gene regulation, and their identification is crucial to the understanding of transcription and gene expression. Traditionally, the isolation and identification of transcription factors has been a long and laborious task. We present here a novel method for the identification of DNA-binding proteins seen in electrophoretic mobility shift assay (EMSA) using the power of two-dimensional electrophoresis coupled with mass spectrometry. By coupling SDS-PAGE and isoelectric focusing to EMSA, the molecular mass and pI of a protein complex seen in EMSA were estimated. Candidate proteins were then identified on a two-dimensional array at the predetermined pI and molecular mass coordinates and identified by mass spectrometry. We show here the successful isolation of a functionally relevant transcription factor and validate the identity through EMSA supershift analysis.  (+info)

(7/9620) A proteomics approach to identify proliferating cell nuclear antigen (PCNA)-binding proteins in human cell lysates. Identification of the human CHL12/RFCs2-5 complex as a novel PCNA-binding protein.

Proliferating cell nuclear antigen (PCNA), a eukaryotic DNA replication factor, functions not only as a processivity factor for DNA polymerase delta but also as a binding partner for multiple other factors. To understand its broad significance, we have carried out systematic studies of PCNA-binding proteins by a combination of affinity chromatography and mass spectrometric analyses. We detected more than 20 specific protein bands of various intensities in fractions bound to PCNA-fixed resin from human cell lysates and determined their peptide sequences by liquid chromatography and tandem mass spectrometry. A search with human protein data bases identified 12 reported PCNA-binding proteins from both cytoplasmic (S100 lysate) and nuclear extracts with substantial significance and four more solely from the nuclear preparation. CHL12, a factor involved in checkpoint response and chromosome cohesion, was a novel example found in both lysates. Further studies with recombinant proteins demonstrated that CHL12 and small subunits of replication factor C form a complex that interacts with PCNA.  (+info)

(8/9620) Peptidomics of the larval Drosophila melanogaster central nervous system.

Neuropeptides regulate most, if not all, biological processes in the animal kingdom, but only seven have been isolated and sequenced from Drosophila melanogaster. In analogy with the proteomics technology, where all proteins expressed in a cell or tissue are analyzed, the peptidomics approach aims at the simultaneous identification of the whole peptidome of a cell or tissue, i.e. all expressed peptides with their posttranslational modifications. Using nanoscale liquid chromatography combined with tandem mass spectrometry and data base mining, we analyzed the peptidome of the larval Drosophila central nervous system at the amino acid sequence level. We were able to provide biochemical evidence for the presence of 28 neuropeptides using an extract of only 50 larval Drosophila central nervous systems. Eighteen of these peptides are encoded in previously cloned or annotated precursor genes, although not all of them were predicted correctly. Eleven of these peptides were never purified before. Eight other peptides are entirely novel and are encoded in five different, not yet annotated genes. This neuropeptide expression profiling study also opens perspectives for other eukaryotic model systems, for which genome projects are completed or in progress.  (+info)

mass spectrometry

  • The new Rockville-based company, called Omic Biosystems, will market a technology called DiART (deuterium (2H) isobaric amine reactive tags) that uses protein tagging designs coupled with sample preparation technology for use in large-scale mass spectrometry proteomics studies. (
  • Informed-Proteomics, a software suite for top-down proteomics analysis, consists of a high-accuracy liquid chromatography-mass spectrometry feature-finding algorithm, an efficient database search to. (
  • Toward a goal of improving patient care, the core offers services and conducts research in the areas of mass spectrometry-based differential proteomics, peptide synthesis, protein and peptide purification, and protein identification, characterization and expression. (


  • NEW YORK (GenomeWeb News) - The University of Maryland Biotechnology Institute said Monday that it has spun out a proteomics venture that will commercialize protein characterization and quantification technology. (
  • Functional proteomics technologies include yeast two-hybrid system for studying protein- protein interactions. (
  • Toxicoproteomics, i.e. the evaluation of protein expression for understanding of toxic events, is an important application of proteomics in preclincial drug safety. (
  • In recent years, proteomics has been used to gain in-depth understanding of many aspects of the host defense against pathogens and has allowed monitoring differences in abundance of proteins as well as posttranscriptional and posttranslational processes, protein activation/inactivation, and turnover. (
  • Proteomics also offers a window to study protein trafficking and routes of communication between organelles. (
  • Proteomics involves the analysis and identification of protein structure and function. (
  • The director of the Proteomics Core is Daniel J. McCormick, Ph.D. Dr. McCormick and his staff have extensive expertise in proteomics and protein chemistry. (


  • With articles written by established leaders in the field as well as by rising stars, this work will be an essential reference tool for all members of genomics, proteomics, transcriptomics and bioinformatics teams, from students, to post-docs, to senior scientists, and a 'must have' for university and research institute libraries. (


  • As Hillis explains it, genomics shows us a list of the ingredients of the body - while proteomics shows us what those ingredients produce. (
  • Use of bioinformatics is essential for analyzing the massive amount of data generated from both genomics and proteomics. (
  • Edited by Lynn Jorde , Peter Little , Mike Dunn and Shankar Subramaniam , this is a fantastic resource that brings together for the first time all four fields of genetics, genomics, proteomics and bioinformatics in an online format for faster delivery of content to meet your dynamic research requirements. (


  • Danny Hills makes a case for the next frontier of cancer research: proteomics, the study of proteins in the body. (


  • Through the Proteomics Core, investigators at Mayo Clinic and elsewhere have access to a broad range of proteomics services, technologies and guidance to help them answer scientific questions. (


  • DUBLIN , Aug. 4, 2015 /PRNewswire/ -- Research and Markets ( ) has announced the addition of Jain PharmaBiotech's new report "Proteomics - Technologies, Markets and Companies" to their offering. (
  • Caprion also has been awarded two consecutive 5-year US$13 million contracts for Biodefense proteomics research in the area of infectious diseases with the NIH-NIAID. (


  • Caprion Proteomics, a privately-held company, is majority owned by Great Point Partners, LP. For more information, please visit: (


  • Establishing a proteomics platform in the industrial setting initially requires implementation of a series of robotic systems to allow a high-throughput approach for analysis and identification of differences observed on 2D electrophoresis gels. (



  • The number of companies involved in proteomics has increased remarkably during the past few years. (