Danielle Swaney

If anyone was curious. We succeeded, but it wasn’t easy. Reviewers were insistent on western blots. Eventually we convinced the editors otherwise using peptide level quant info to show decent sequence coverage and a biochemical/biophysical rational for why not all the peptides had the same quant.

I have been thinking about this question too. Part of me was worried that doing this would damage the entire system in a way that will be used against scientists to justify further reductions.

Welcome to the club 😔. You’ve got a big voice. Hopefully you can continue to advocate strongly for science—particularly with your local representatives and community members where changed minds can have a meaningful impact.

I hear you. If this was a well-studied protein with a rock-solid antibody I might consider it. But it’s not. Also, it’s an antiquated double standard to “validate” more specific and quantitative proteomics data with an inferior western blot assay. I would bet the opposite request is far more rare.

How are people handling the “validate your protein change by western blot” reviewer request? We already have proteomics data showing protein KD, qPCR showing transcript KD, and a dramatic functional response. I am leaning towards holding my ground not to do western. It is just redundant busy work

Usually it’s one 10cm or 15cm dish of cells. But this is way more than needed, since we only inject ~5% of the sample after IP.

Affinity Purification Mass Spectrometry on the Orbitrap-Astral Mass Spectrometer Enables High-Throughput Protein-Protein Interaction Mapping - PubMed Classical proteomics experiments offer high-throughput protein quantification but lack direct evidence of the spatial organization of the proteome, including protein-protein interaction (PPIs) network...

After a 15 year hiatus, I’ve got a new paper with the Coon lab. Led by @liaserrano.bsky.social, we kicked the tires on the Orbitrap Astral for PPI studies. Since we run thousands of APMS samples/yr we focused on fast analysis (7 min run, >200 samples in 29hr). pubmed.ncbi.nlm.nih.gov/40025722/

👏 Philly was a great host city. Women-friendly state laws, easy train ride from the airport to the city, and most of all the people of the city were so nice and helpful. 10/10 would go again.

Thanks for the shoutout on our paper. It was a difficult process of methods optimization over several years to get this to work well and provide biologically meaningful results.