# How to access/run correlations on proteomics data

**URL:** <https://forum.depmap.org/t/how-to-access-run-correlations-on-proteomics-data/3923>\
**Category:** Issues and Bugs\
**Created:** [January 21, 2025, 4:15pm UTC](https://forum.depmap.org/t/how-to-access-run-correlations-on-proteomics-data/3923 "2025-01-21T16:15:36Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Ruth\_Kieran](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/ruth_kieran/32/1403_2.png) [@Ruth\_Kieran](https://forum.depmap.org/u/Ruth_Kieran)\
**Post date:** [January 21, 2025, 4:15pm UTC](https://forum.depmap.org/t/how-to-access-run-correlations-on-proteomics-data/3923/1 "2025-01-21T16:15:36Z")

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Hi  
I have been trying to correlate drug sensitivity with RPPA expression of ERBB2\_py1248 across cell lines.  
I used to do this by selecting custom analysis, then gene ERBB2, then I could select proteomics for ERBB2\_py1248, which would give me volcano plots for whatever drug screen I selected, e.g. GDSC1.  
Something seems to have changed in the last few weeks, I am not seeing the proteomics as a dataset option. I am not sure if it is moved or if I can still access it another way?  
Thanks very much

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**Author:** ![Ruth\_Kieran](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/ruth_kieran/32/1403_2.png) [@Ruth\_Kieran](https://forum.depmap.org/u/Ruth_Kieran)\
**Post date:** [January 24, 2025, 10:59am UTC](https://forum.depmap.org/t/how-to-access-run-correlations-on-proteomics-data/3923/2 "2025-01-24T10:59:44Z")

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Edit: it seems like this data should be in the harmonized RPPA CCLE or MS CCLE datasets but I don’t see the py1248 data there, only typical ERBB2/Her2  
Very grateful if anyone has any ideas

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**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [January 28, 2025, 2:25pm UTC](https://forum.depmap.org/t/how-to-access-run-correlations-on-proteomics-data/3923/3 "2025-01-28T14:25:50Z")

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Hi Ruth,

In 24Q4, we replaced the existing proteomic datasets in Data Explorer with a “harmonized” version where all proteomics datasets 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. We are planning to support post-translational modification in the future if we get more PTM-level datasets, but in the meantime, the original MS and RPPA data are still available and can be accessed in the “downloads” page.

Thanks,

Simone