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HUPO-PSI / usi

Universal Spectrum Identifier for Mass Spectrometry
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"USI not found at any of the repositories!" appears when using Universal Spectrum Identifier in ProteomeXchange? #3

Open ATU-SZ opened 1 year ago

ATU-SZ commented 1 year ago

Dear Professor

Sorry for disturbing you. I'd like to ask you a question. 

The Universal Spectrum identifiers is a very professional tool. I recently used Universal Spectrum identifiers to look up the PSM, but clicking "look up USI" kept saying "USI not found at any of the repositories!" (Universal Spectrum Identifier // ProteomeXchange). But I have checked the relevant information and there is no mistake, and tried other USIs under this project are not running.

I found that the USI that can be looked up successfully displays "Updated project metadata" in "2014" in the column of DATASET HISTORY in the information page of the corresponding project.

For example: mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_05_2Feb12_Cougar_11-10-09.mzML:scan:12298:[iTRAQ4plex]-LHFFM[Oxidation]PGFAPLTSR/3

The " Updated project metadata in 2014" is not displayed in the DATASET HISTORY column of the project which can not be looked up successfully.

For example: mzspec:PXD006512:CNHPP_HCC_LC_profiling_L006_P_F1:scan:64442:VADALTNAVAHVDDMPNALSALSDLHAHK/3

mzspec:PXD006201:20150804SL_Qe2_HEP2_UBISITE_rep1_A_15_HpH_6:scan:15223:TLSDYNIQK[UNIMOD:1290]/2

I guess if some PSM could not be displayed on USI because there was no "Updated project metadata". Will the tool be able to update project metadata on all projects in the future?

Can you help me with this problem?  Relevant information is provided below

Thanks for your attention and time.

Screenshot information-1 Screenshot information-2 Screenshot information-3

edeutsch commented 1 year ago

Hi @ATU-SZ thank you for your post and interest in the USI. I think the issue that you are finding of unresolvable USIs is not related to metadata updates. Metadata updates should not affect a USI. The PeptideAtlas message "DatasetNotHere" means that the data are not at PeptideAtlas, at least under than PXD. PeptideAtlas has some datasets that were submitted to PRIDE, but not all of them.

Ideally PRIDE would furnish these, they are only able to provide USIs for some datasets, and they have been having some infrastructure problems of late that prevent servicing of USI requests.

If the PXD006201 dataset is of particular interest, we can get it over here at PeptideAtlas and then PeptideAtlas can provide those USIs.

Is that dataset of particular interest?