I've spent some time wondering how many people out there have been successful in single cell proteomics and not known they were. I think it's fair to say that the data processing is still more convoluted than bulk lysate proteomics and it's possible to get great LCMS data and not gotten the most out of the single cell data.
This might be particularly easy to do with DIA-NN which takes longer to process files with lower over all signal to noise ratios. I was working on tutorial videos over the holiday break, but then my voice failed entirely so I only got through DIA-NN and SpectroNaut (which....the latter is probably unnecessary). Now, the end goal of these videos is also to visualize the single cell results in our lab's downstream solution, SCP-Viz, but as noted in the videos you can just stop watching when we get to a simple GUI that can actually make sense of the data, if you'd rather do something much harder. 😇
How to process single cell data with DIA-NN is here. (Doing it this way you're talking about maybe 5 minutes/cell you analyze using a very standard12 threads of a 16 thread desktop PC)
One way to process single cell data with SpectroNaut is here (it is faster to do something similar to what I do with DIA-NN above, but in the new versions there isn't that big of a gap between that and just dumping all your data in as shown here.
If you're interested in QC'ing your single cell proteomics data post-acquisition and pre-processing and/or cleaning those files of spectra that don't have your single cell reporter ions, as detailed recently here -
Next up on my list is how to process DDA single cell data in FragPipe, MaxQuant and Proteome Discoverer and I'll add them to the OrsburnLab youtube channel and to my Github as I pull them together.
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