|Affinity purification mass spectrometry||Affinity purification is the capture of biological material via specific enrichment with a ligand coupled to a solid support. Many types of ligands can be used in affinity purification, including DNA and RNA molecules (most often oligonucleotides), chemicals, lipids, peptides, or proteins, with some of the most widely used ligands for affinity purification being antibodies.
In AP-MS, a single protein or molecule of interest is affinity captured in a matrix as bait. A protein mixture (often a lysate from the cell or tissue of interest) is passed through the matrix, and interacting partners (prey) are retained by interaction with the bait. Proteins that do not interact pass through the matrix and are discarded. There are multiple variations in the affinity purification step, including immunoprecipitation and pull-down of epitope tagged molecules.
Once purified, proteins can be processed for direct analysis by MS or, fractionated to reduce sample complexity. |
|Annotation||The process of attaching additional information to biological entities. Annotation can be structural (i.e. identification of the elements from a sequence, such as protein coding regions or the location of regulatory motifs) or functional (i.e. adding biological information to the identified elements, such as the biological function of a protein domain or an entire protein, or the molecular interactions or regulatory role of a nucleotide sequence). Annotation can either be applied automatically or can be manually added (in a process called 'curation') from various sources, such as the scientific literature. Annotation can either be applied automatically or it can be curated (manually) from the scientific literature. At EMBL-EBI, we use a combination of automatic and manual annotation to enrich our databases. |
|Domain||Independently stable tertiary structures of proteins. They are distinct functional and/or structural units and can evolve, exist and function independently. |
|IMEx Consortium||A collaboration of interaction databases which have agreed to share curation on protien interactions and to create a single, non-redundant set of records available to the research community. |
|Identifier||A string given to a biological data entity (to allow reference, retrieval and tracking the entity). Identifiers are usually stable but some entities can change 'identifier' when they are moved between databases. In such cases a stable [Accession] can be used instead to refer to the same entity regardless of database |
|IntAct||An EBI-hosted database of molecular interactions. Most of the interactions hosted in IntAct are protein–protein interactions. IntAct represents the interactions with a high level of detail, following the guidelines of the International Molecular Exchange (IMEX) Consortium. http://www.ebi.ac.uk/intact/ |
|PSICQUIC||PSICQUIC is a project led by the HUPO Proteomics Standard Initiative (HUPO-PSI) that aims to standardise programmatic access to molecular interaction databases. A single query can access multiple databases using the PSICQUIC web service. |
|Protein–protein interaction||Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. |
|Proteome||A proteome is a set of proteins produced in an organism, system, or biological context. We may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver). The proteome is not constant; it differs from cell to cell and changes over time. To some degree, the proteome reflects the underlying transcriptome, however protein activity is also modulated by many factors in addition to rates of production. |
|Proteomics||Proteomics is the large-scale study of proteomes. A proteome is a set of proteins produced in an organism, system, or biological context. We may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver). |
|UniProt||UniProt – Universal Protein Resource: The world's most comprehensive catalogue of information on proteins and a central repository of protein sequence and function, created by joining the information contained in UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and PIR http://www.ebi.ac.uk/uniprot/ |
|curation||In the context of biological databases, curation is the process of interpreting and representing biological data using standardised annotation, controlled vocabularies and standardised formats, so the data can be stored and made available to the scientific community. |
|curator||A professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases. The role of a biocurator encompasses quality control of primary biological research data intended for publication, extracting and organizing data from original scientific literature, and describing the data with standard annotation protocols and vocabularies that enable powerful queries and biological database inter-operability. Curators communicate with researchers to ensure the accuracy of curated information and to foster data exchanges with research laboratories. |
|interactome||In molecular biology an Interactome is defined as the whole set of molecular interactions in cells. Specifically it means physical interactions among molecules but can also mean indirect interactions among genes. |