Wednesday, March 22, 2023

A lot of single cell proteomic variation is cell size!


How to normalize single cell proteomics data has been a hot topic this week on social media for some reason. I went to link a blog post on this study from Lanz et al., and discovered I'd never actually posted this preprint, even though I've cited it and used their method of normalization.

Considering my Inbox has so many items thumbtacked at the top with red exclamation points I have to scroll down to see anything new, I probably shouldn't have time to post this. HAHA, I'm going to do something I actually want to for 6 minutes today! 

What this group did was attempt to identify normalization factors that would remove some of the variance in single cell measurements in two recent datasets. What they found was that if they simply normalized the histone H4 abundance between cells, a lot of the variability condensed. 

I can say for sure that it definitely helps. For anyone using Proteome Discoverer this is easy to set up. 

You reprocess your consensus report and you make these changes in either of the quantification nodes. You set it for specific protein amount and then you choose the FASTA file of the protein that you want to normalize against. This FASTA must be recognizable as a main FASTA by PD (imported through the admin tab). 

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