This article or section is in need of attention from an expert on the subject. WikiProject Molecular and Cellular Biology or the Molecular and Cellular Biology Portal may be able to help recruit one. If a more appropriate WikiProject or portal exists, please adjust this template accordingly. The journal Proteomics covers topics including whole proteome analysis of organisms, protein expression profiling, disease, pharmaceutical, agricultural and biotechnological applications, and analysis of cellular systems, organelles and protein complexes. ... Image File history File links Emblem-important. ...

Robotic preparation of MALDI mass spectrometry samples on a sample carrier.

Proteomics is the large-scale study of proteins, particularly their structures and functions.^[1][2] Proteins are vital parts of living organisms, as they are the main components of the physiological pathways of cells. The term "proteomics" was coined to make an analogy with genomics, the study of the genes. The word "proteome" is a portmanteau of "protein" and "genome". The proteome of an organism is the set of proteins produced by it during its life, and its genome is its set of genes. Image File history File linksMetadata Download high-resolution version (1024x768, 258 KB)[edit] Summary Public domain image from cancer. ... Image File history File linksMetadata Download high-resolution version (1024x768, 258 KB)[edit] Summary Public domain image from cancer. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulfur. ... A DNA microarray Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein!) functions and interactions. ... Cells in culture, stained for keratin The cell is the structural and functional unit of all living organisms. ... Genomics is the study of an organisms entire genome; Rathore et al, . Investigation of single genes, their functions and roles is something very common in todays medical and biological research, and cannot be said to be genomics but rather the most typical feature of molecular biology. ... For other uses, see Gene (disambiguation). ... A portmanteau (IPA: ) is a word or morpheme that fuses two or more words or word parts to give a combined or loaded meaning. ... The term proteome was coined by Mark Wilkins in 1995 (1) and is used to describe the entire complement of proteins in a given biological organism or system at a given time, i. ...

Proteomics is often considered the next step in the study of biological systems, after genomics. It is much more complicated than genomics, mostly because while an organism's genome is rather constant, a proteome differs from cell to cell and constantly changes through its biochemical interactions with the genome and the environment. One organism has radically different protein expression in different parts of its body, different stages of its life cycle and different environmental conditions. Another major difficulty is the complexity of proteins relative to nucleic acids. E.g., in human there are about 25 000 identified genes but an estimated >500 000 proteins that are derived from these genes. This increased complexity derives from mechanisms such as alternative splicing, protein modification (glycosylation,phosphorylation) and protein degradation. In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... The term proteome was coined by Mark Wilkins in 1995 (1) and is used to describe the entire complement of proteins in a given biological organism or system at a given time, i. ... Biochemistry is the study of the chemical processes in living organisms. ... Protein expression is a subcomponent of gene expression. ... Look up nucleic acid in Wiktionary, the free dictionary. ... Glycosylation is the process or result of addition of saccharides to proteins and lipids. ... A phosphorylated serine residue Phosphorylation is the addition of a phosphate (PO4) group to a protein or a small molecule or the introduction of a phosphate group into an organic molecule. ...

Scientists are very interested in proteomics because it gives a much better understanding of an organism than genomics. First, the level of transcription of a gene gives only a rough estimate of its level of expression into a protein. An mRNA produced in abundance may be degraded rapidly or translated inefficiently, resulting in a small amount of protein. Second, many proteins experience post-translational modifications that profoundly affect their activities; for example some proteins are not active until they become phosphorylated. Methods such as phosphoproteomics and glycoproteomics are used to study post-translational modifications. Third, many transcripts give rise to more than one protein, through alternative splicing or alternative post-translational modifications. Finally, many proteins form complexes with other proteins or RNA molecules, and only function in the presence of these other molecules. The interaction of mRNA in a eukaryote cell. ... Posttranslational modification means the chemical modification of a protein after its translation. ... Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing phosphate as a post-translational modification. ... Glycoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing carbohydrates as a post-translational modification. ... Various modes of alternative splicing Alternative splicing is the process that occurs in eukaryotes in which the splicing process of a pre-mRNA transcribed from one gene can lead to different mature mRNA molecules and therefore to different proteins. ...

Since proteins play a central role in the life of an organism, proteomics is instrumental in discovery of biomarkers, such as markers that indicate a particular disease. Biomarker is an occasionally used synonym for biosignature, which is a term used in astrobiology to indicate a measurable phenomenon that indicates the presence of life. ...

With the completion of a rough draft of the human genome, many researchers are looking at how genes and proteins interact to form other proteins. A surprising finding of the Human Genome Project is that there are far fewer protein-coding genes in the human genome than proteins in the human proteome (20,000 to 25,000 genes vs. > 500,000 proteins). The human body may even contain more than 2 million proteins, each having different functions. The protein diversity is thought to be due to alternative splicing and post-translational modification of proteins. The discrepancy implies that protein diversity cannot be fully characterized by gene expression analysis, thus proteomics is useful for characterizing cells and tissues. This article is about modern humans. ... The Human Genome Project (HGP) is a project undertaken with a goal to understand the genetic make-up of the human species by determining the DNA sequence of the human genome and the genome of a few model organisms. ...

To catalog all human proteins, their functions and interactions is a great challenge for scientists. An international collaboration with these goals is co-ordinated by the Human Proteome Organization (HUPO). The Human Proteome Organization (HUPO) is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. ...

Studying proteomics

Most proteins function in collaboration with other proteins, and one goal of proteomics is to identify which proteins interact. This often gives important clues about the functions of newly discovered proteins. Several methods are available to probe protein-protein interactions. The traditional method is yeast two-hybrid analysis. New methods include protein microarrays, immunoaffinity chromatography followed by mass spectrometry, and combinations of experimental methods such as phage display and computational methods. Overview of two-hybrid assay as follows. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... A chemist using column chromatographic apparatus in the mid-1950s Affinity chromatography is a method of separating biochemical mixtures, based on a highly specific biologic interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand. ... Mass spectrometry (previously called mass spectroscopy (deprecated)[1] or informally, mass-spec and MS) is an analytical technique used to measure the mass-to-charge ratio of ions. ...

Current research in proteomics requires first that proteins be resolved, sometimes on a massive scale. Protein separation can be performed using two-dimensional gel electrophoresis, which usually separates proteins first by isoelectric point and then by molecular weight. Protein spots in a gel can be visualized using a variety of chemical stains or fluorescent markers. Proteins can often be quantified by the intensity of their stain. Once proteins are separated and quantified, they are identified. Individual spots are cut out of the gel and cleaved into peptides with proteolytic enzymes. These peptides can then be identified by mass spectrometry, specifically matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry. In this procedure, a peptide is placed on a matrix, which causes the peptide to form crystals^{[citation needed]}. Then the peptide on the matrix is ionized with a laser beam and an increase in voltage at the matrix is used to shoot the ions toward a detector in which the time it takes an ion to reach the detector depends on its mass. The higher the mass, the longer the time of flight of the ion. In a MALDI-TOF mass spectrometer, the ions can also be deflected with an electrostatic reflector that also focuses the ion beam. Thus, the masses of the ions reaching the second detector can be determined with high precision and these masses can reveal the exact chemical compositions of the peptides, and therefore their identities. Two-dimensional gel electrophoresis, commonly abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. ... The isoelectric point (pI) is the pH at which a molecule or surface carries no net electrical charge. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Matrix-Assisted Laser Desorption/Ionization (MALDI) is a soft ionization technique used in mass spectrometry, allowing, among others, to ionise biomolecules (biopolymers like proteins, peptides and sugarchains) which tend to be more fragile and quickly lose structure when ionised by more conventional ionisation methods. ... For other uses, see Laser (disambiguation). ...

Protein mixtures can also be analyzed without prior separation. These procedures begin with proteolytic digestion of the proteins in a complex mixture. The resulting peptides are often injected onto a high pressure liquid chromatography column (HPLC) that separates peptides based on hydrophobicity. HPLC can be coupled directly to a time-of-flight mass spectrometer using electrospray ionization. Peptides eluting from the column can be identified by tandem mass spectrometry (MS/MS). The first stage of tandem MS/MS isolates individual peptide ions, and the second breaks the peptides into fragments and uses the fragmentation pattern to determine their amino acid sequences. Labeling with isotope tags can be used to quantitatively compare proteins concentration among two or more protein samples. Chromatography is a family of analytical chemistry techniques for the separation of mixtures. ... Electrospray (nanoSpray) ionization source Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions. ...

One of the most promising developments to come from the study of human genes and proteins has been the identification of potential new drugs for the treatment of disease. This relies on genome and proteome information to identify proteins associated with a disease, which computer software can then use as targets for new drugs. For example, if a certain protein is implicated in a disease, its 3D structure provides the information to design drugs to interfere with the action of the protein. A molecule that fits the active site of an enzyme, but cannot be released by the enzyme, will inactivate the enzyme. This is the basis of new drug-discovery tools, which aim to find new drugs to inactivate proteins involved in disease. As genetic differences among individuals are found, researchers expect to use these techniques to develop personalized drugs that are more effective for the individual.

A computer technique which attempts to fit millions of small molecules to the three-dimensional structure of a protein is called "virtual ligand screening". The computer rates the quality of the fit to various sites in the protein, with the goal of either enhancing or disabling the function of the protein, depending on its function in the cell. A good example of this is the identification of new drugs to target and inactivate the HIV-1 protease. The HIV-1 protease is an enzyme that cleaves a very large HIV protein into smaller, functional proteins. The virus cannot survive without this enzyme; therefore, it is one of the most effective protein targets for killing HIV.

There are many distributed computing programs, such as the world community grid, which allows people around the world to help scientists by computing calculations. The software adds to the use of super computers by using the unused processing power of millions of home computers. The world community grid works on HIV, cancer, and protein folding. All three projects centre around protein modelling and protein modification models. Using the data gained from distributed computing models of proteins, scientists can develop more specific and effective therapies. In addition, most enzymes act as part of complexes and networks, which also affect the way an enzyme acts in a cell. Understanding these complex networks will assist in developing drugs that affect the function of these complexes. The official World Community Grid logo World Community Grid is an effort to create the worlds largest public computing grid to tackle scientific research projects that benefit humanity. ...

Biomarkers

Understanding the proteome, the structure and function of each protein and the complexities of protein-protein interactions will be critical for developing the most effective diagnostic techniques and disease treatments in the future.

An interesting use of proteomics is using specific protein biomarkers to diagnose disease. A number of techniques allow to test for proteins produced during a particular disease, which helps to diagnose the disease quickly. Techniques include western blot, immunohistochemical staining, enzyme linked immunosorbent assay (ELISA) or mass spectrometry. The following are some of the diseases that have characteristic biomarkers that physicians can use for diagnosis: Immunohistochemical staining is a common immunological technique used in the biological sciences for the detection of proteins within the context of the tissue in which the protein is found. ... This article or section does not adequately cite its references or sources. ... Mass spectrometry (previously called mass spectroscopy (deprecated)[1] or informally, mass-spec and MS) is an analytical technique used to measure the mass-to-charge ratio of ions. ...

• In Alzheimer’s disease, elevations in beta secretase creates amyloid/beta-protein, which causes plaque to build up in the patient's brain, which causes dementia. Targeting this enzyme decreases the amyloid/beta-protein and so slows the progression of the disease. A procedure to test for the increase in amyloid/beta-protein is immunohistochemical staining, in which antibodies bind to specific antigens or biological tissue of amyloid/beta-protein.
• Heart disease is commonly assessed using several key protein based biomarkers. Standard protein biomarkers for CVD include interleukin-6, interleukin-8, serum amyloid A protein, fibrinogen, and troponins. cTnI cardiac troponin I increases in concentration within 3 to 12 hours of initial cardiac injury and can be found elevated days after an acute myocardial infarction. A number of commercial antibody based assays as well as other methods are used in hospitals as primary tests for acute MI.
• Proteomic analysis of kidney cells and cancerous kidney cells is producing promising leads for biomarkers for renal cell carcinoma and developing assays to test for this disease. In kidney-related diseases, urine is a potential source for such biomarkers. Recently, it has been shown that the identification of urinary polypeptides as biomarkers of kidney-related diseases allows to diagnose the severity of the disease several months before the appearance of the pathology.Article

Alzheimers disease (AD) or primary dementia of Alzheimers type is an incurable, degenerative neuropsychiatric disease which results in a pervasive loss of first mental, then physical functioning due to the deterioration of brain tissue. ... Renal cell carcinoma is the most common form of kidney cancer arising from the renal tubule. ...

Branches

1. Protein separation. Proteomic technologies rely on the ability to separate a complex mixture so that individual proteins are more easily processed with other techniques.
2. Protein identification. Well-known methods include low-throughput sequencing through Edman degradation. Higher-throughput proteomic techniques are based on mass spectrometry, commonly peptide mass fingerprinting on MALDI-TOF instruments, or De novo repeat detection MS/MS on instruments capable of more than one round of mass spectrometry. MS/MS data can be analyzed by simple database searches as is the case for PMFs and additionally they can be analyzed by de novo sequencing and homology searching. This particular approach allows to even identify similar (homolog) proteins, e.g. across species in case a protein was derived from an organism with unsequenced genome. Antibody-based assays can also be used, but are unique to one sequence motif.
3. In quantitative proteomics different methods are used to obtain quantitative information on a proteome-wide scale. Rather than just lists of proteins, quantitative proteomics provides functional information and reveals temporal changes in the proteome.
4. Protein sequence analysis is a branch of bioinformatics that deals with searching databases for possible protein or peptide matches by algorithms such as Mascot, PEAKS(software), OMSSA, SEQUEST and X!Tandem, PWB Protein Identification Cluster Software Solution, functional assignment of domains, prediction of function from sequence, and evolutionary relationships of proteins.
5. Structural proteomics concerns the high-throughput determination of protein structures in three-dimensional space. Common methods are x-ray crystallography and NMR spectroscopy.
6. Interaction proteomics concerns the investigation of protein interactions on the atomic, molecular and cellular levels. see related article on Protein-protein interaction prediction.
7. Protein modification studies the modified forms of proteins. Almost all proteins are modified from their pure translated amino-acid sequence, by so-called post-translational modification. Specialized methods have been developed to study phosporylation (phosphoproteomics) and glycosylation (glycoproteomics).
8. Cellular proteomics is a new branch of proteomics aiming to map the location of proteins and protein-protein interactions in whole cells during key cell events. Centers around the use of techniques such as X-ray Tomography and optical fluorescence microscopy.
9. Experimental bioinformatics is a branch of bioinformatics, as it is applied in proteomics, coined by Mathias Mann. It involves the mutual design of experimental and bioinformatics methods to create (extract) new types of information from proteomics experiments.

Edman degradation, developed by Pehr Edman, is a method of sequencing amino acids in a peptide. ... Mass spectrometry (previously called mass spectroscopy (deprecated)[1] or informally, mass-spec and MS) is an analytical technique used to measure the mass-to-charge ratio of ions. ... Peptide mass fingerprinting (also known as protein fingerprinting) (PMF) is an analytical technique for protein identification that was developed by John Yates and colleagues (3). ... Prediction of the amino acid sequence from peptide fragment masses of a protein obtained by a Mass spectrometry measurement. ... The aim of quantitative proteomics is to obtain quantitative information about all proteins in a sample. ... Mascot is a software search engine that uses mass spectrometry data to identify proteins from primary sequence databases. ... PEAKS is a popular tandem mass spectrometry software designed for peptide sequencing and protein identification. ... There are very few or no other articles that link to this one. ... X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... Pacific Northwest National Laboratorys high magnetic field (800 MHz) NMR spectrometer being loaded with a sample. ... This article is being considered for deletion in accordance with Wikipedias deletion policy. ... Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing phosphate as a post-translational modification. ... Glycoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing carbohydrates as a post-translational modification. ...

Technologies

Proteomics uses various technologies:

• One- and two-dimensional gel electrophoresis is used to identify the relative mass of a protein and its isoelectric point.
• X-ray crystallography and nuclear magnetic resonance are used to characterize the three-dimensional structure of peptides and proteins. However, low-resolution techniques such as circular dichroism, Fourier transform infrared spectroscopy and Small angle X-ray scattering (SAXS) can be used to study the secondary structure of proteins.
• Tandem mass spectrometry combined with reverse phase chromatography or 2-D electrophoresis is used to identify proteins using database search tools such as Mascot, PEAKS(software), OMSSA, X!Tandem and SEQUEST or de novo algorithms and quantify all the levels of proteins found in cells.
• Scaffold, a software tool useful in visualization of tandem mass spectrometry results.
• Tandem mass spectrometry combined with tagging technologies such as TMT, ICPL or ITRAQ is used for quantification of proteins and peptides.
• Mass spectrometry (no-tandem), often MALDI-TOF, is used to identify proteins by peptide mass fingerprinting. This technology is also used in so-called "MALDI-TOF MS protein profiling" where samples (i.e. serum) are prepared by either protein chips (SELDI-TOF MS), magnetic beads (The Bruker Daltonics protein profiling platform) or with other methods of sample treatment, such as liquid chromatography, size-exclusion and immunoaffinity. Protein peaks of interest must be identified by tandem mass spectrometry. Protein profiling with MALDI-TOF MS could be of high use in clinical diagnostics, but so far there has been little success with advancing MALDI-TOF MS protein profiling into clinical validation due to high analytical variation.
• ICP-MS combined with MeCAT - Metal Coded Tagging - technology is used for ultrasensitive quantification of proteins and peptides down to low attomol range
• Affinity chromatography, yeast two hybrid techniques, fluorescence resonance energy transfer (FRET), and Surface Plasmon Resonance (SPR) are used to identify protein-protein and protein-DNA binding reactions.
• X-ray Tomography used to determine the location of labeled proteins or protein complexes in an intact cell. Frequently correlated with images of cells from light based microscopes.
• Software based image analysis is utilized to automate the quantification and detection of spots within and among gels samples. While this technology is widely utilized, the intelligence has not been perfected yet. For example, the leading software tools in this area tend to agree on the analysis of well-defined, well-separated protein spots, but they deliver different results and tendencies with less-defined less-separated spots - thus necessitating manual verification of results.

Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid, ribonucleic acid, or protein molecules through an electric charge. ... The isoelectric point (pI) is the pH at which a molecule or surface carries no net electrical charge. ... X-ray crystallography, also known as single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules. ... NMR redirects here. ... Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Circular dichroism (CD) is a form of spectroscopy based on the differential absorption of left- and right-handed circularly polarized light. ... FTIR of a thin film of ethanol in the liquid phase. ... SAXS (small-angle X-ray scattering) is a small-angle scattering (SAS) technique where the elastic scattering of X-rays (wavelength 0. ... Mass spectrometry is a technique for separating ions by their mass-to-charge (m/z) ratios. ... A HPLC. From left to right: A pumping device generating a gradient of two different solvents, a steel enforced column and an apparatus for measuring the absorbance. ... Two dimensional gel electrophoresis, commonly abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. ... Mascot is a software search engine that uses mass spectrometry data to identify proteins from primary sequence databases. ... PEAKS is a popular tandem mass spectrometry software designed for peptide sequencing and protein identification. ... There are very few or no other articles that link to this one. ... Mass spectrometry is a technique for separating ions by their mass-to-charge (m/z) ratios. ... Tandem Mass Tags (TMT) are chemical labels used for mass spectrometry (MS) based quantitation and identification of biological macromolecules, especially, proteins, peptides and nucleic acids. ... Mass spectrometry (previously called mass spectroscopy (deprecated)[1] or informally, mass-spec and MS) is an analytical technique used to measure the mass-to-charge ratio of ions. ... Matrix-Assisted Laser Desorption/Ionization (MALDI) is a soft ionization technique used in mass spectrometry, allowing, among others, to ionise biomolecules (biopolymers like proteins, peptides and sugarchains) which tend to be more fragile and quickly lose structure when ionised by more conventional ionisation methods. ... Peptide mass fingerprinting (also known as protein fingerprinting) (PMF) is an analytical technique for protein identification that was developed by John Yates and colleagues (3). ... Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is method of analyzing a complex mixture of proteins. ... ICP-MS (Inductively coupled plasma mass spectrometry) is a type of mass spectrometry that is highly sensitive and capable of the determination of a range of metals and several non-metals at concentrations below one part in 1012. ... Affinity chromatography is a biochemical separation method that combines size fractionation capability of gel permeation chromatography with the ability to design a stationary phase that reversibly binds to a known subset of molecules. ... This page meets Wikipedias criteria for speedy deletion. ... Fluorescent proteins localize the guanosine 5-triphosphate hydrolase ARF in the Golgi apparatus of a living macrophage. ... X-ray Tomography is a branch of X-ray microscopy. ... Image analysis is the extraction of meaningful information from images; mainly from digital images by means of digital image processing techniques. ...

See also

• bioinformatics
• cytomics
• genomics
• List of omics topics in biology
• metabolomics
• lipidomics
• Shotgun proteomics
• Top-down proteomics
• Bottom-up proteomics
• systems biology
• transcriptomics
• phosphoproteomics
• PEGylation

Map of the human X chromosome (from the NCBI website). ... Cytomics is the study of cell systems (cytomes) at a single cell level. ... Genomics is the study of an organisms entire genome; Rathore et al, . Investigation of single genes, their functions and roles is something very common in todays medical and biological research, and cannot be said to be genomics but rather the most typical feature of molecular biology. ... ÎŽThis is a navigational and informational list. ... Metabolomics is the systematic study of the unique chemical fingerprints that specific cellular processes leave behind - specifically, the study of their small-molecule metabolite profiles. ... Lipidomics is the large-scale study of non-water-soluble metabolites (lipids). ... Shotgun proteomics is a method of identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry. ... Top-down proteomics is 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. ... Bottom-up proteomics is a method for the identification of proteins in complex mixtures through a combination of two-dimensional gel electrophoresis and mass spectrometry. ... Systems biology is a term used very widely in the biosciences, particularly from the year 2000 onwards, and in a variety of contexts. ... The Transcriptome is the set of all mRNA molecules (or transcripts) in one or a population of biological cells for a given set of environmental circumstances. ... Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing phosphate as a post-translational modification. ... Polyethylene glycol // In 1970s, pioneering research by Davis, Abuchowski and colleagues foresaw the potential of the conjugation of Polyethylene glycol (PEG) to Proteins. ...

Protein databases

• UniProt
• PIR
• Swiss-Prot
• PDB
• NCBI
• Human Protein Reference Database

UniProt is the universal protein database, a central repository of protein data created by combining Swiss-Prot, TrEMBL and PIR. This makes it the worlds most comprehensive resource on protein information. ... The introduction of this article does not provide enough context for readers unfamiliar with the subject. ... Swiss-Prot is a curated biological database of protein sequences created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and the European Bioinformatics Institute. ... The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... The HPRD provides a comprehensive link to any queried protein The Human Protein Reference Database is a protein database accessible through internet. ...

References

A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ...

Bibliography

External links

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Proteomics

At Wikiversity you can learn more and teach others about Proteomics at:

The Department of Proteomics

• In-Gel Digestion Protocol for Mass Spectrometry and Proteomics Studies
• deltaMasses - Post-translational modification detection after mass spectrometry
• YRC Public Data Repository - Public data repository of experimental mass spectrometry, yeast two-hybrid, localization, protein structure prediction and large-scale protein complex prediction data from many organisms.
• GPMDB is a database of results obtained from protein identification experiments.
• PRIDE (PRoteomics IDEntifications database) is a centralized, standards compliant, public data repository for proteomics data.
• Human Proteinpedia - portal for sharing and integration of human protein data.
• Human Protein Reference Database - a manually curated human protein database from literature allowing users to add data by using an annotation system called Human Proteinpedia.
• Yeast GFP Localization Database - Database of microscope images and quantitation for most of the yeast proteome.
• Sashimi is a SourceForge repository for open source proteomic software.
• The NCRR proteomics resource at PNNL is a source of easy to use software (executables and source code) and data related to LC-MS based analysis pipelines.
• PRIDE proteome database is a public repository for digital content relating to proteomics.
• IntAct Interaction Database is a public repository for manually curated molecular interaction data from literature.
• BioGRID: A General Repository for Interaction Datasets, is a public repository for manually curated molecular interaction data from literature.
• CPAS Fred Hutchinson Cancer Research Center open source software platform for processing and mining proteomics data, a development funded by the FHCRC, National Cancer Institute, and the Canary Foundation.
• msInspect FHCRC developed open source tool for mining LC-MS data, including peptide detection and quantitation.
• Human Protein Atlas
• Rosetta@home GRID Computing. Determining the 3-dimensional shapes of proteins
• Protein Fluoresence and Structure Toolkit PFASTProtein fluorescence, structural and statistical-correlation analysis on-line.

Image File history File links Broom_icon. ... Image File history File links Wikibooks-logo-en. ... Wikibooks logo Wikibooks, previously called Wikimedia Free Textbook Project and Wikimedia-Textbooks, is a wiki for the creation of books. ... Image File history File links Wikiversity-logo-Snorky. ... Wikiversity logo Wikiversity is a Wikimedia Foundation beta project[1], devoted to learning materials and activities, located at www. ... Human Proteinpedia is a portal for sharing and integration of human proteomic data. ... Genomics is the study of an organisms entire genome; Rathore et al, . Investigation of single genes, their functions and roles is something very common in todays medical and biological research, and cannot be said to be genomics but rather the most typical feature of molecular biology. ... Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus). ... // Overview Polyploid (in Greek: πολλαπλόν - multiple) cells or organisms contain more than two copies (ploidy) of their chromosomes. ... Glycomics, or glycobiology is a discipline of biology that deals with the structure and function of oligosaccharides (chains of sugars). ... The Human Genome Project (HGP) is a project undertaken with a goal to understand the genetic make-up of the human species by determining the DNA sequence of the human genome and the genome of a few model organisms. ... Chemogenomics can be defined as a genomic response to chemical compounds. ... Structural genomics or structural bioinformatics refers to the analysis of macromolecular structure particularly proteins. ... The terms pharmacogenomics and pharmacogenetics tend to be used interchangeably, and a precise, consensus definition of either remains elusive. ... Pharmacogenomics is the branch of pharmacology which deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drugs efficacy or toxicity. ... Toxicogenomics is a form of analysis by which the activity of a particular toxin or chemical substance on living tissue can be identified based upon a profiling of its known effects on genetic material. ... Modern genomics has been deined in many ways: * The study of genomes. ... Map of the human X chromosome (from the NCBI website). ... Cheminformatics (also known as chemoinformatics and chemical informatics) is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. ... Systems biology is a term used very widely in the biosciences, particularly from the year 2000 onwards, and in a variety of contexts. ...