Universal Spectrum Identifier


(updated 2021-07-29)

The Universal Spectrum Identifier is multi-part key identifier for identifying mass spectra contained in public data repositories, primarily focused on proteomics. A USI such as mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_05_2Feb12_Cougar_11-10-09.mzML:scan:12298:[iTRAQ4plex]-LHFFM[Oxidation]PGFAPLTSR/3 encodes the dataset, the MS Run, the scan number and the proposed peptidoform and charge of the ions responsible for the spectrum. Such an identifier enables communication and verification of important spectral evidence.

The Universal Spectrum Identifier (USI) specification completed the PSI Document Process in July of 2021 and is now ratified by the PSI.  Funding for development was 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.

An article describing the USI has been published in Nature Methods and is also available in bioRxiv.

Universal Spectrum Identifier FINISHED Specification

The USI specification has been ratified by the PSI and is complete. Current documents are available here:

- USI specification document 1.0: [PDF] [GitHub]

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

- Current GitHub repository for USI-related materials

- An article describing the USI has been published in Nature Methods and is also available in bioRxiv.


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