Hello,

I am currently doing a search for proteomic data on rheumatoid arthritis studies. I find Proteomexchange a great start, but find some publications don't upload their raw data. To try and find as much data as possible I am also searching through PubMed using "Proteomics" and "mass spectrometry" as additional filters. This helps in finding data that hasn't been relased as raw files. It is usually formatted in excel sheets as the outputs of MaxQuant etc, including the LFQ values.

Hope this helps a little.

Go here; http://www.proteomexchange.org/

then to the bottom of the page where they list partner repositories. You'll find several listed. They hold different types of data.

The main problem I find with some data submitted is the lack of "metadata." ie. They have uploaded 50 files, named file_1 to file_50. They do not include ANY info about what the runs represent, so it's essentially useless.

Hi Peter,

There is also

1. MassIVE which is curated by University of California San Diego, USA. It is under the Center for Computational Mass Spectrometry of UC San Diego.

https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp

Once a deposition is under "complete", with peak files matching raw files and mzID results files, the MassIVE will also register/ produce ProteomeExchange number which may be required by some journals.

2. Another resource is "GPM" or Generalized Proteomics data Meta-analysis

https://www.thegpm.org/GPMDB/index.html

Best,

Hediye.