Some people seem to like the Bravo AssayMap, which has enrichment protocols using their proprietary cartridges and also autoSP3. There are several protocols using the Opentrons 2, but they aren't necessarily directly transferable compatible with the OT Flex, which also requires special tips.

I had the opportunity to present MAETi, which enables #immunopeptidomics profiling of 10,000 cells. I was very happy to see that there is a lot of interest on it since @julbeyr.bsky.social , PhD student at Stefan Tenzer lab, has done a lot of great work optimizing it to reach these levels.

Megan Ford did an excellent job presenting our antibody-based workflow for high-throughput #immunopeptidomics of low-input cell and clinical samples. A big thanks to @dgpf.bsky.social sponsoring her travel award that made her assistance possible.

It felt like a big milestone to come back to France to present our work at the Immunopeptidomics Platform and Tenzer Lab HI-TRON Mainz, 7.5 years after my PhD in Paris:

Thanks a lot to the organizers and all the people who made it such a great experience. Merci beaucoup!
EuPA, FPS, and @ypic.bsky.social

It depends on several factors: main application, budget, availability of service engineers in your region. Are your samples scarce? Do you aim for high-throughput? Mostly cell/tissue lysates or also plasma? Only proteomics or also peptidomics?

If 21k UP is consensus while 63k UP includes isoforms, the redundancy in the latter may result in lower cut-off.
I guess that >100 AAs includes 21k UP while the others include 63k UP. If that's the case, I do see the upwards trend.
Note aside, I would plot cut-off (dependent variable) in y axis