Danielle Swaney
@dlswaney.bsky.social
Associate Professor at UCSF, visiting scientist at the Gladstone Institutes. Expertise in mass spectrometry and proteomics. Views are my own. profiles.ucsf.edu/danielle.swaney
Did you know 🦑 squids dynamically re-write proteins via RNA-editing? Like A LOT! In work led by Jack Moen, we show this reshape protein stability, localization, PTMs, etc.; revealing how RNA-editing dramatically expands protein diversity to tune function in unexpected ways. doi.org/10.64898/202...
Functional diversification of the cephalopod proteome by RNA-editing
Coleoid cephalopods exhibit the highest levels of ADAR-mediated RNA editing of any known animal, yet the functional consequences of most recoding events remain largely unknown. We integrate proteomics...
doi.org
December 17, 2025 at 6:12 PM
Did you know 🦑 squids dynamically re-write proteins via RNA-editing? Like A LOT! In work led by Jack Moen, we show this reshape protein stability, localization, PTMs, etc.; revealing how RNA-editing dramatically expands protein diversity to tune function in unexpected ways. doi.org/10.64898/202...
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.
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
September 18, 2025 at 7:04 PM
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.
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
May 14, 2025 at 5:32 PM
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
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/
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...
pubmed.ncbi.nlm.nih.gov
March 4, 2025 at 3:14 PM
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/