Ben Parker Lab

This is an important letter! We often do ‘omics analysis and each of the 1000’s of analytes measured has its own power calculation which is impossible to predict.

So cool and so many research questions from these data! @savitski-lab.bsky.social -lab.bsky.social

Big thanks to @unimelbcmr.bsky.social and many others!

Phosphoproteomics of aged insulin-resistant bone identifies P70S6K phosphorylation of AFF4 as a gene-specific transcriptional regulator - Nature Communications Insulin signaling plays a crucial role in coordinating skeletal development with whole‑body energy metabolism. Here, the authors use phosphoproteomics to show insulin-signaling rewiring in aged, insul...

Our #phosphoproteomics analysis of insulin signaling in bone uncovered a new mechanism of transcriptional activation via S6K phosphorylation of AFF4. It appears to play a role in regulating the expression of genes in ageing and insulin resistance. www.nature.com/articles/s41...

This looks fun and super easy! Thanks! Do you have to run all existing QC runs with new runs simultaneously in a single search? Or can you add new QC search results of day only a few files to existing searches?

Thanks @nickescott.bsky.social @unimelbcmr.bsky.social and many others

Quantitative interactome mapping of skeletal muscle insulin resistance Protein-protein interactions (PPIs) are dynamic and critical to adaptive homeostasis. While there have been massive efforts to catalogue proteome-wide PPIs, global quantification of changes remains a ...

Protein:protein interactions are incredibly dynamic so how do we quantify and discover changes in native tissues? Our new study uses qXL-MS and PCP-MS to study dynamic remodeling of interactions following skeletal muscle insulin resistance. #MyoBlue #Proteomics www.biorxiv.org/content/10.6...

Yes but the issue is false positives with phosphorylated Ser/Thr. A cocktail of phosphatases combined with mild beta-elimination may reduce this… www.sciencedirect.com/science/arti...

It’s interesting that the 8600 doesn’t appear to be marketed with single cell capabilities compared to other vendors. I wonder why SCIEX didn’t at least have a note in this space?

Two weeks to go before the abstract deadline (July 18th)! Looking forward to seeing you all there!

Skeletal muscle proteomics: considerations and opportunities npj Metabolic Health and Disease - Skeletal muscle proteomics: considerations and opportunities

Are you interested in #proteomics and #skeletalmuscle? It can be a real pain to get deep reproducible coverage. Check out our review with @adeshmukh.bsky.social We analyse some considerations including current limitations and how to potentially overcome them #myoblue @unimelbcmr.bsky.social

👩‍💻 We’re hiring! Lê Cao Lab at Uni Melbourne @mig-unimelb.bsky.social needs an R dev to power the next-gen of mixOmics 🚀
Love #RStats, #Bioconductor & multi-omics? Help expand mixOmics, run workshops & publish cutting-edge methods.
Apply: unimelb.wd105.myworkdayjobs.com/en-US/UoM_Ex...

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This sounds fantastic and can’t wait to try it on some new peptidomics data!

Congratulations Atul and team! Amazing body of work.

Yes probably redundant, but there are considerations before pushing back. Do you have lysate remaining or would you have to repeat experiments? How many other ‘battles’ are there in the comments? If there are bigger fights and you have lysate than might be worth a ‘quick’ WB to appease the gods.

Thanks for all the support @unimelbcmr.bsky.social!!

Big thanks to all our collaborators for making this wok possible. @unimelbcmr.bsky.social @craigagoodman1.bsky.social and many others…

Why do we care? Because we have previously shown that UFC1 levels are negatively correlated with lean mass in various mouse strains, and knockdown of UFC1/UFMylation can increase muscle function. Maybe myosin UFMylation is a key link? elifesciences.org/articles/82951

We quantified UFMylation in the above human biopsies revealing several increased UFMylation sites including Myosins! Additional mapping of sites on Myosins reveal they are extensively modified, and in silico modelling suggest sites adjacent to ATP binding plays a functional role.

What did we find?... A whole bunch of cool substrates including UFMylation of Myosins which we validate following knockdown of UFC1 (the E2 ligase) in vivo combined with TMT-16plex labelling and LC-MS/MS…

In collaboration with CST, we developed antibodies that recognise "remnant ValGly" left on UFM1-conjugates following tryptic digestion. Similar to the remnant ubiquitin "diGly" approach published by www.cell.com/molecular-ce...

However, check out this anti-UFM1 blot from control muscle biopsies and people with ALS... A big band at 30kDa (probably RPL26) but clearly more to discover including big heavy bands >250kDa!

UFMylation is a ubiquitin like modification of UFM1 applied to substrate lysine residues. <15 substrates have been identified (a nice summary: www.cell.com/molecular-ce.... RPL26 has been most extensively characterised and suggested to be the major substrate…

Site-specific quantification of the in vivo UFMylome reveals myosin modification in ALS UFMylation is the post-translational modification of Ubiquitin Fold Modifier1 (UFM1) applied to substrate proteins. Blazev et al. develop an antibody-based enrichment approach followed by LC-MS/MS to ...

Check out our new #proteomic method to site-specifically quantify UFMylation! We applied the approach to look at human skeletal muscle biopsies from #ALS. A great collaboration with CellSignalTechnology and many others...
A little summary below... www.cell.com/cell-reports...

Very nice indeed. In this example does LLOQ=LLOD?

Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!

The grant agencies in Australia seem to specifically announce outcomes on Friday afternoons. I think the idea is so you can cool off over the weekend. However, better than Monday morning!

Running a genetic stop sign accelerates oxygen metabolism and energy production in horses Horses are among nature’s greatest athletes, yet the ancestral molecular adaptations fueling their energy demands are poorly understood. Within a clinically important pathway regulating redox and meta...

Our newest paper is out in Science! This riddle took 5 years to solve. Genome annotation and AI missed it. Manual inspection and serendipity still have advantages for cracking nature's secrets! With @science.org @evolutionvu.bsky.social @rokaslab.bsky.social

www.science.org/doi/10.1126/...

Yes, this is where things are interesting. All databases produce similar number of total peptides. Large db’s identify more novel peptides missing in canonical db but the larger search space and requirement for higher score at 1%FDR means peptides get filtered out.