In my lab they are about to publish a manuscript I haven't been involved. They have proteomics data and they want to deposit it in a public database. I found several databases to publish proteomics data (PRIDE and ZENODO mostly). However, It is not clear to me how to do it in PRIDE:
I have Olink data but I don't know how to classify it for its submission to PRIDE. The options it gives me are:
- top-down proteomics,
- shotgun proteomics,
- gel-based proteomics,
- cross-linking (CX-MS),
- affinity purification (AP-MS),
- SRM/MRM,
- SWATH MS (data independent acquisition) .
I've searched several articles but most don't publish their Olink data, and some published it in the company website (which I don't know how to do it).
I'm more familiar with the RNA-seq data repositories and a search for the type of technology used by Olink didn't help. What is the best place to deposit this data?
Here is the header in case it might help deciding
Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink INFLAMMATION(v.3021) Olink NEURO EXPLORATORY(v.3911) Olink NEUROLOGY(v.8012)
patients week IL8 VEGFA CD8A MCP-3 GDNF CDCP1 CD244 IL7 OPG LAP TGF-beta-1 uPA
A02w1_1 1 5,6806 9,67399 9,76328 1,83557 2,46947 3,67568 7,77966 3,982 9,43218 7,80715 9,51527
