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Ben Parker Lab @benparkerlab.bsky.social · 12d

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?

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Reposted by Ben Parker Lab

Komander Lab @komanderlab.bsky.social · Jul 4

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

Rashmi Agrata @rashmiagrata.bsky.social · Jul 4

Australia’s First Ubiquitin Summit is here! 🥳
📍Lorne, Victoria | 🗓️ 20–23 November 2025

Join us on the scenic coastline of Lorne for 4 days of cutting-edge ubiquitin science, featuring a fantastic lineup of international speakers covering all corners of the Ub world—from mechanisms to therapeutics

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Ben Parker Lab @benparkerlab.bsky.social · Jul 3

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

Skeletal muscle proteomics: considerations and opportunities

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

www.nature.com

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Reposted by Ben Parker Lab

Kim-Anh Lê Cao @mixomics.org · Jun 23

👩‍💻 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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Reposted by Ben Parker Lab

Yasset Perez-Riverol @ypriverol.bsky.social · Jun 18

🚨 Has PRIDE helped your research?

Take 15 mins to tell funders why open data matters!
📊 Fill out the EMBL-EBI 2025 survey 👉
www.surveymonkey.com/r/QGFMBH8?ch...

Your feedback helps keep PRIDE open, FAIR & impactful.
🙏 Please share!
#FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE

This link will take you to a page that’s not on LinkedIn

lnkd.in

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Ben Parker Lab @benparkerlab.bsky.social · Jun 6

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

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Ben Parker Lab @benparkerlab.bsky.social · May 27

Congratulations Atul and team! Amazing body of work.

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Ben Parker Lab @benparkerlab.bsky.social · May 14

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.

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Ben Parker Lab @benparkerlab.bsky.social · May 11

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

Ben Parker Lab @benparkerlab.bsky.social · May 11

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

Ben Parker Lab @benparkerlab.bsky.social · May 11

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

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Ben Parker Lab @benparkerlab.bsky.social · May 11

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.

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Ben Parker Lab @benparkerlab.bsky.social · May 11

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…

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Ben Parker Lab @benparkerlab.bsky.social · May 11

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...

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Ben Parker Lab @benparkerlab.bsky.social · May 11

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!

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Ben Parker Lab @benparkerlab.bsky.social · May 11

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…

https://doi.org/10.1016/j.molc…

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Ben Parker Lab @benparkerlab.bsky.social · May 11

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...

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 ...

www.cell.com

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Ben Parker Lab @benparkerlab.bsky.social · May 8

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

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Reposted by Ben Parker Lab

Alexey Nesvizhskii @nesvilab.bsky.social · May 5

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!

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Ben Parker Lab @benparkerlab.bsky.social · Apr 11

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!

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Reposted by Ben Parker Lab

The Castiglione Lab @ Vanderbilt @castiglionelab.bsky.social · Mar 28

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/...

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...

www.science.org

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Ben Parker Lab @benparkerlab.bsky.social · Mar 22

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.

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Ben Parker Lab @benparkerlab.bsky.social · Mar 22

Yes, I think you are right. The different databases have different levels of redundancy. I’ll search some variant databases to confirm. Thank you!

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Ben Parker Lab @benparkerlab.bsky.social · Mar 21

Hi #proteomics people, I'm hoping someone can help interpret these results. We have generated .fasta from RNAseq. We are testing the effects of different db size on min score cut-off @ 1% FDR. Hypothesis: as db increase, score increases. We don't see this with multiple algorithms and appears random.

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Ben Parker Lab @benparkerlab.bsky.social · Mar 18

Congratulations and nice collection of spirits 👌

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