I am trying to do proteomics of rare cells populations and I need to collect say 100K cells from 5ml of media after FACS. I am looking for a simple and efficient method, preferable not based on centrifugation (since the pellets are way to small to see) to quickly collect the cells. I understand filtration might be the best option and I tested
https://www.mcponline.org/content/early/2019/02/21/mcp.RA118.001259
this protocol from Broad, but the filters sometimes block, which is a problem. Any suggestions?
So you do not have the option to cell sort and isolate on your flow cytometer?
It may be easiest to find a nearby institute that does and ask to borrow their facilities.
I would cell sort. If you don't have a cell sorter there will be someone that have one and you can put the cells straight back into culture. Make sure you have a good medium that will keep your cells happy.
I am not sure I understood your question, but It looks like you need to FACS-sort your cells. If your staining/gating strategy is relatively straightforward and you need a enrichment / depletion of certain cell populations, you should consider a bead-based selection system (there are options both for positive and negative markers and dead cell depletion).
For example: https://www.miltenyibiotec.com/US-en/products/macs-cell-separation/cell-separation-reagents/microbeads-and-isolation-kits.html#gref
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