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Glossary/Terms: Atlas nomenclature Protein ID terms

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Terms used in PeptideAtlas

Atlas Build A collection of peptides identified in samples from a particular species or subproteome (e.g. plasma). Each build is constructed by searching spectra against a sequence database and/or a spectral library, assigning probabilities to the resulting peptide-spectrum matches (PSMs), then selecting PSMs that pass a threshold. Atlas builds have names like Human Plasma PeptideAtlas 2009-11.
Default Build Each organism or subproteome is assigned a generic default build name, such as Human Plasma. This name usually refers to the latest build for that organism or subproteome, even though in some cases older builds are available. When using the Search functionality, only default builds can be searched. In some contexts, tables of build information can be restricted to show only default builds.
Biosequence Name In PeptideAtlas, Biosequence Name refers to a protein name that a peptide has been mapped to. A given peptide sequence may have been found in more than one biosequence or more than once in the same biosequence. (For example, human peptide sequence ACNPQYAGAIVVHCSAGVGR maps to Ensembl Biosequence Names ENSP00000342783, ENSP00000314568, ENSP00000348468, ENSP00000216877, and ENSP00000351559, plus eight biosequences from IPI and Swiss-Prot.) Because of the redundancy within Ensembl and between Ensembl and other sequence databases used in PeptideAtlas, many biosequences are identical, or highly similar, to other biosequences.
Best Probability All peptide identifications have been put through the PeptideProphet program to assign identification probabilities. The best probability is the best P observed for the peptide sequence.
Intron Spanning Peptide that begins on one exon but ends on another exon
Number of Protein Mappings Number of biosequences the peptide sequence has been identified within. Some of these may be identical or highly similar.
Number of Times Observed The number of times a peptide sequence has been identified in all experiments.
Number of Unique Locations on Genome The number of unique chromosomal locations for the mapped peptide sequence. If a peptide sequence has not been found in the protein database, this value will be zero and there will not be a Biosequence Name for this peptide.
Peptide Name/Accession The PeptideAtlas designated name consists of PAp followed by 8 numbers. Each accession corresponds to a unique peptide sequence.
Sample A description of the experiment including details such as extraction, digestion, preparation. (Sample annotation is still in progress, but expect to see minimal description of sample for all samples, and more information for those published or declared public).
Start/End Position Chromosomal coordinates of the peptide sequence.