Skip to content

Latest commit

 

History

History
36 lines (26 loc) · 2.49 KB

CollectionIdentifiers.md

File metadata and controls

36 lines (26 loc) · 2.49 KB
Raw

USI Collection Identifiers

The Universal Spectrum Identifier (USI) for Mass Spectrometry has as its second field a collection identifier. The specification itself does not prescribe the complete list of allowable collection identifiers. Rather, the list is maintained here at GitHub and is extensible in an open manner without changing the specification.

Permitted Collection Identifiers:

  1. PXDnnnnnn - The preferred collection identifier is of the form PXDnnnnnn, such as PXD017269 (http://proteomecentral.proteomexchange.org/dataset/PXD017269). The PXDnnnnnn SHOULD be used for all proteomics mass spectrometry datasets that have been registered at ProteomeXchange.

  2. MSVnnnnnnnnn - A collection identifier for datasets contained at the MassIVE repsository, such as MSV000078556. This type of identifier SHOULD only be used when there is not a corresponding PXDnnnnnn identifier for the dataset, as is often the case for metabolomics datasets.

  3. RPXDnnnnnn - A ProteomeXchange identifier for a reprocessed dataset of the form RPXDnnnnnn, such as RPXD006668 (http://proteomecentral.proteomexchange.org/dataset/RPXD006668). The RPXDnnnnnn SHOULD ONLY be used when there is no corresponding PXDnnnnnn identifier available (as in the case where an RPXDnnnnnn dataset derives from a non-ProteomeXchange dataset) or in the context of a PSM identifier

  4. RMSVnnnnnnnnn - A collection identifier for reprocessed datasets contained at the MassIVE repsository, such as RMSV000078556. This type of identifier SHOULD ONLY be used when there is not a corresponding PXDnnnnnn identifier for the dataset, since PXDnnnnnn identifiers are preferred.

  5. USI000000 - A collection identifier to be used as a placeholder for an as-yet unknown collection identifier. In cases where a USI must be written at a time when the final collection identifier is not yet known, a placeholder of USI000000 SHOULD be used, so as to enable a straightforward search and replace when the final PXD number or other collection identifier is registered. Software implementations should recognize this string as a placeholder that needs to be resolved.

  6. PXLnnnnnn - A ProteomeXchange spectral library identifier of the form PXLnnnnnn. All spectral libraries registered through ProteomeCentral are given a PXLnnnnnn identifier. These collections contain representative spectra often aggregated from several replicates, rather than original scan events in MS datasets as denoted by PXDnnnnnn identifiers.

There are no other approved collection identifiers at this time.