Quantifying proteins from archived tissue continues to improve. #proteomics www.biorxiv.org/content/10.1... - ThreadSky

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harrisons.bsky.social • 100 days ago

Quantifying proteins from archived tissue continues to improve. #proteomics

https://www.biorxiv.org/content/10.1101/2024.11.17.624038v1

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lgamon.bsky.social•100 days ago

Very nice work but not sure if this protein yield is right. Paper seems to suggest this is four replicates of individual 10µm sections. Slightly implausible for a single tissue section. I wish I got yields like that!!

harrisons.bsky.social•100 days ago

Do you think leftover paraffin fragments could interfere with the measurement?

lgamon.bsky.social•100 days ago

Perhaps. Hasn’t been a problem in our hands though. Back of the envelope calculation suggests a 1cm x 2cm x 10um ‘box’ of HeLa cells should be max 600ug of protein (no losses, no gaps between cells) so my guess is it’s either an overestimate, or they used multiple sections for that figure 🤷‍♂️

itsbinir.bsky.social•100 days ago

A general question here.. isn't HeLa cell around 30 um in diameter on average?? so 10um sections means partial cells spread across the section??

harrisons.bsky.social•100 days ago

I think Luke is taking the volume of the box divided by the volume of a (spherical) HeLa cell times the protein in a HeLa cell to get that protein estimate.

But yeah, those cells are slice n diced! :D

itsbinir.bsky.social•99 days ago

Cool.. Sliced Cell Proteomics.. Now I am wondering whether there could be a difference based on longitudinal or latitudinal slicing in protein content and distribution..

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