Universal Spectrum Identifier

Status

(updated 2021-05-20)

A revised draft of the Universal Spectrum Identifier (USI) specification has been completed and resubmitted to the PSI Document Process. This means that the ratification process is nearing completion but has not been finalized. Feedback is still welcome. Funding for development is being provided by the US NIH National Institute of General Medical Sciences under grant R24 GM127667. Please contact psidev-ms-dev@lists.sourceforge.net with questions and comments.

Universal Spectrum Identifier UNfinished Specification

The USI specification has been resubmitted to the PSI Document Process after addressing reviewer comments, but has still not been ratified and community feedback and discussion are welcome. Current documents are available here:

- USI specification document DRAFT 10: [docx] [PDF] [GitHub]

- Companion ProForma (Proteoform and Peptidoform Notation) draft specification (PDF)

The next step is waiting for final phase of the PSI Document Process to complete

- Current GitHub repository for USI-related materials

- There is a draft manuscript describing the proposed standard available on bioRxiv

Examples

Here are a view specific examples of USIs that link to various resources that are starting to implement them:

- Link to ProteomeCentral for mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555:VLHPLEGAVVIIFK/2

- Link to PeptideAtlas for mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555:VLHPLEGAVVIIFK/2

- Link to MassIVE for mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555:VLHPLEGAVVIIFK/2

- Link to PRIDE  for mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_12_5Feb12_Cougar_11-10-11.mzML:scan:11850:[UNIMOD:214]YYWGGLYSWDMSK[UNIMOD:214]/2

- Link to jPOST for mzspec:PXD005175:CRC_iTRAQ_06:scan:11803:VEYTLGEESEAPGQR/3

Tools that support the USI:

- ProteomeCentral USI aggregator USICentral- PeptideAtlas (see example above)

- MassIVE (see example above)

- jPOST (see example above)

- PRIDE (see example above)

- Trans-Proteomic Pipeline spectrum viewer (http://www.tppms.org/)

- PDV integrative proteomics data viewer (https://github.com/wenbostar/PDV)

- Universal Spectrum Explorer (https://www.proteomicsdb.org/use/)

- Python Pyteomics support (https://pyteomics.readthedocs.io/en/latest/api/usi.html)

- Pyteomics usage example

- Metabolomics Spectrum Identifier Resolver (https://metabolomics-usi.ucsd.edu/)

- PROXI spectrum schema (https://github.com/HUPO-PSI/proxi-schemas/tree/master/specs)

 

Annotated USI Examples