Nicola Zamboni

Postdoctoral Researcher - Metabolomics

We are hiring. The geekier, the better!
jobs.ethz.ch/job/view/JOP...

Amazing dataset describing the metabolic profiles of 66 E. coli transporter knockouts by @sulheim.bsky.social with Peter Doubleday and @nzamboni.bsky.social. The tool, set up by @lambdapp.bsky.social and Eric Ulrich allows you to explore for yourself. Enjoy! Pre-print here: doi.org/10.1101/2025...

This project wouldn't been possible without Peter Doubleday and @nzamboni.bsky.social at @imsb-eth.bsky.social. Peter conducted >10,000 mass spec analyses 🤯. So grateful for this opportunity to team up with the best of the best in metabolomics 😍

Read more: www.biorxiv.org/content/10.1...

#microsky

Well-deserved recognition for the amazing teamwork. The launch was a real blast. I am already curious about the next one 🤩.

Optimisation of electron-induced dissociation parameters for molecular annotation of glycerides and phospholipids in fast LC-MS Electron-induced dissociation methods, particularly electron impact excitation of ions from organics (EIEIO), offer enhanced capabilities for lipid structural elucidation over traditional collision-in...

In the latest issue of ‪Analyst:
Optimisation of electron-induced dissociation parameters for molecular annotation of glycerides and phospholipids in fast LC-MS.
#OpenAccess from Nicola Zamboni et al @nzamboni.bsky.social @alaaothman.bsky.social @ethz.ch Read now: pubs.rsc.org/en/content/a...

Height! Even though it's not the most correct, it's the most robust to obtain consistent spectral intensitied across the full dynamic range, i.e. on the 8600.
Most importantly: stick to "moderate smoothing" and "drop single values".

Available to read now via Open Access:
pubs.rsc.org/en/content/a...
Fast, general-purpose metabolome analysis by mixed-mode liquid chromatography–mass spectrometry
Nicola Zamboni et al @nzamboni.bsky.social @alaaothman.bsky.social @ethz.ch
#MassSpec

We are beyond happy to see so many contributions from the #SIRIUScommunity at tat #Metabolomics2025. Don't miss the opportunity to get in touch and gain first-hand insights how you can integrate SIRIUS into your annotation workflow.

8600_data polybox - Use it as a logical memory stick, store your data on the ETH campus!

I've been asked about my slides on the #ZenoTOF8600. We uploaded the poster, which includes the data and comments, plus all key data and results at polybox.ethz.ch/index.php/s/.... Feel free to reshare or to ping me for more.

No OrbiTOF? Bummer. Or maybe it's how you get the AT to benchtop? OT-OTOF 🫶

👍 but hard to say more with so many "under defined conditions"

This was funny until I realized I am the one who has to prove it. 👀👀

You don't have to redistribute the dlls with mzmine. Leave it to the users. You already request users to install pwiz to convert raw data, and that comes with acceptance of vendors' licensing terms. Just look for the class and, if available, call it. Seems legit to me.

??? Any user can get the dotnet libs via pwiz or directly from the SCIEX website, fulfilling all licensing terms.

💯

... them to take an active lead in data processing. They are also planning to better document their dotnet api for reading files. I assume we will hear more at ASMS.

I just spoke to a SCIEX executive and am less worried. They say that afficionados of pwiz, skyline, msdial, mzmine... won't be affected in their capacity to use their favourite tool, neither in the short nor in the long run. There are, however, numerous new developments that motivate...

Too bad your MRM module isn't. It would solve some of the concerns re skyline. 😬

GitHub - MannLabs/alpharaw: An open-source Python package to unify raw MS data accession and storage. An open-source Python package to unify raw MS data accession and storage. - MannLabs/alpharaw

Using the dll, or wrappers like
github.com/MannLabs/alp...

Ok, the answer just came in: they are developing their own converter. ETA late 2025. Good luck to all.

PS2: I am confident that mzio will be happy to provide wiff support in the pro version 😜

Exactly. I can't comment on PRM worklows, but this will have major implications for all high-res users.
PS: good thing we already switched to reading data directly from wiff skipping pwiz and mzML ;-).

This doesn't make any sense. SCIEX doesn't offer any viale alternative to pwiz for exporting data, or did I miss something?

They already failed to correctly export EAD data, but this seems a complete killer for their own business.

Join me on June 2 to enter a new dimension and discover its incredible #value. 4000+ injections don't lie.

🤭 x3

If it's HRMS, let's move beyond sensitivity or other silly specs.

It's "easy" to build more sensitive instruments, but it typically comes at the cost of dynamic range, speed, or robustness. IRL, we need the full package all the time.

A study using an n=1 experiment with single standards at 0V CID reported that 70% of detected ions were in-source fragments (ISFs). www.nature.com/articles/s42... This finding was extrapolated to suggest that ISFs affect all metabolomics experiments to this degree. A counterpoint. rdcu.be/ebFwc 1/n

Discovery of metabolites prevails amid in-source fragmentation - Nature Metabolism Nature Metabolism - Discovery of metabolites prevails amid in-source fragmentation

I'm happy to share a correspondence in @naturemetabolism.bsky.social in which I was involved. #metabolomics #lipidomics www.nature.com/articles/s42...