Universal Spectrum Identifier


(updated 2020-10-01)

A working draft of the Universal Spectrum Identifier (USI) specification has been completed and submitted to the PSI Document Process. This means that the ratification process has begun but has not been finalized. Feedback is still very much 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 submitted to the PSI Document Process, but has still not been ratified and community feedback and discussion is welcome. Current documents are available here:

- USI specification document DRAFT 7: [docx] [PDF] [GitHub]

- Companion ProForma (Proteoform and Peptidoform Notation) draft specification (Google doc)

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

- Current GitHub repository for USI-related materials


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

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

- PeptideAtlas (see example above)

- MassIVE (see example above)

- jPOST (see example above)

- PRIDE (see example above)

- ProteomeCentral (http://proteomecentral.proteomexchange.org/devED/cgi/spectra?usi=mzspec:PXL000006:02-14-2019:index:1250)

- IPSA fork, in development (https://kusterlab.github.io/IPSA/PeptideAnnotator.html)


Annotated USI Examples