Hi Lars and Dunja,
Lars: I only see fluorescence flow experimental info in the Methods in that Nat. Methods paper.....though your point stands.
Dunja: There's also the PLAYR paper (
http://dx.doi.org/10.1038/nmeth.3742), which does CyTOF using both protein and RNA targets.
One great thing about the PLAYR paper is that the researchers (to their credit) demonstrate that RNA and protein levels aren't always correlated (eg, Figure 3E, ITGAX).
This was also seen with MET in this paper (
https://doi.org/10.1186/s13059-016-1045-6), which used anti-protein antibodies with primer tags for proximity extension readouts along with the RNA (see Fig 3 and following discussion) Also, this paper (doi: 10.1038/s41598-017-03057-5) had some other cases of good or poor correlation between mRNA and protein levels.
Therefore, I think you have to be careful about the idea that scRNASeq and protein-based CyTOF *have* to agree, or that if they don't, one is "wrong". There's a vast amount of literature on transcriptional regulation vs translational regulation, how many proteins a given RNA molecule makes (and the occasional long-tail outliers), and the relative rates of degradation of the RNA and the protein it codes for (I'm a protein biochemist by training, so I'm a bit biased
.
Mike