Phospho-Proteomics data accessibility issue

Dear DepMap Team,
Couple of weeks ago, I was able to access and download phospho-proteomics data from the DepMap interface, for classical signalling nodes, such as EGFR, AKT, MAPK… etc for which the phospho-status on few key residues was available in every cell line. However now it seems that the data are not accessible anymore, do you know what happened ?
Many thanks,
Charly

Hi Charly,

Could you provide more details on what datasets you are trying to download and how?

In 24Q4, we created a “harmonized” version of proteomic datasets where all matrices are indexed by the same identifier (uniprot ID). This allows users to make more direct comparisons between different datasets, however, we do realize that a small portion of proteins had to be dropped to achieve this harmonization.

While these harmonized datasets are being displayed in the data explorer, all the original files containing all the PTM information are still available in the “Downloads” page. If you navigate to Downloads > All Data and search the file names of interest, you should still be able to access them.

Hope this helps,
Simone

Dear Simone,
Many thanks for your reply
Basically, on the depmap portal, I could for example enter a gene name like AKT1, then I go to the characterization tab, where I can download expression data, methylation data, copy number data … etc that related to this gene. However before there use to be a phospho-AKT1 Serine 473 tab from which I could download the data in order to obtain the phospho status of this protein across the 1000 cell lines profiled. The downloaded dataset name was : Akt_pS473 Protein Array
However this is not there anymore.
and I was able to download phospho status of many protein this way, like S6K, EGFR, SHP2… etc however it seems all gone now for the user friendly interface.
I can have a look at the original files then and I see what I can do,
If you figured out what happened, let me know,
Thanks again,
Have a nice day,
Charly

Hi Charly,

Thanks for sharing how you were able to access this data in the interface.

Sounds like the dataset you were interacting with was the CCLE RPPA data. If you go to Downloads > All Data and search “Protein Array (RPPA)”, you should be able to find and download the RPPA data table. Let me know if that doesn’t have what you’re looking for.

Thanks,
Simone