SomaLogic data to PRIDE Archive

[ypriverol]

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Description

I'm the team coordinator of PRIDE team (www.ebi.ac.uk/pride/), the largest proteomics database, part of ProteomeXchange. We have multiple users asking us to submit SomaLogic data to PRIDE, something is not yet supported. I found this repository from SomaLogic open in github and want to contact you for help.

We are modeling now how in PRIDE, how Somalogic data should look like, this is the first prototype:

SomaScan: 
    RAW data: 
    - .adat: raw adat file provided by SomaLogic
        - Examples: 
            - SS-217041.raw.adat: raw adat file provided by SomaLogic
            - SS-217041.hybNorm.medNormInt.plateScale.calibrate.anmlQC.qcCheck.anmlSMP.adat: fully normalized adat file provided by SomaLogic
        Search Results: 
    - .txt: search results and quantification results ()
        - Examples:
            - RFU_raw.txt: RFU matrix extracted from SS-217041.raw.adat
            - RFU_hyb.txt: RFU matrix after hyb normalization
            - RFU_hyb.msnCal.txt: RFU matrix after hyb.msnCal normalization
            - RFU_[hyb.msnCal.ps.txt](http://hyb.msncal.ps.txt/): RFU matrix after [hyb.msnCal.ps](http://hyb.msncal.ps/) normalization
            - RFU_[hyb.msnCal.ps.cal.txt](http://hyb.msncal.ps.cal.txt/): RFU matrix after [hyb.msnCal.ps.cal](http://hyb.msncal.ps.cal/) normalization
            - RFU_[hyb.msnCal.ps.cal.msnAll.txt](http://hyb.msncal.ps.cal.msnall.txt/): RFU matrix after [hyb.msnCal.ps.cal.msnAll](http://hyb.msncal.ps.cal.msnall/) normalization
    Others Files:
    - sample.txt: sample metadata (including normalization scale factors)
    - somamer.txt: SOMAmer metadata (including normalization scale factors)
    - plate.txt: plate metadata (including normalization scale factors)

These are the requested files we are planning to ask to the submitters for the community to be able to reproduce the results. Can you give us some feedback or help us about which data we should ask.

Thanks a lot in advance. Yasset

Priority Level

• [ ] High
• [x] Medium
• [ ] Low

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Thank you for using SomaDataIO :pray:!

[stufield]

Thank you! I'll forward this to our engagement team.

[ypriverol]

@stufield I have the meeting today with someone from the company. I will close this issue. Thanks for your support.