Matthias Trost

Trucks loaded up for the lab move. Next stop, Manchester!

Quite amazing how much stuff is in a lab.

Will UKRI’s funding buckets shore up UK research’s sandcastle? Academics’ concerns are mounting as news drips out of the research councils about cuts and freezes ahead of a major funding restructuring intended to promote interdisciplinarity and transparency. But ...

I am rather worried that this government not only will actively fail UK universities but also screw over one of the gems of UK economy - science and life science, particularly.

Will UKRI's funding buckets shore up UK research? share.google/B92vQ7E6nEOK...

A real pleasure to examine @emmottlab.bsky.social 's first PhD student. Well done, Stephen!

Congrats to Dr @stephenholmes.bsky.social on passing his PhD viva today! Thanks to examiners Al Darby and @mtrost.bsky.social!

I have a 3-year postdoc position available at University of Manchester for a mass spec expert in proteomics. The person will be involved in exciting projects in single cell proteomics, drug discovery and innate immunity - on timsTOF Ultra AIP & HF & Astral Zoom.

www.jobs.ac.uk/job/DQJ093/r...

We have a 18 months Post-Doctoral Research Associate position available funded by the Kennedy Trust for a Mass Spectrometry/Proteomics expert at the @officialuom.bsky.social

This is a collaborative position with the Rice lab @grainofscience.bsky.social

www.jobs.manchester.ac.uk/Job/JobDetai...

We were not aware of Triqler and will compare it. One difference is rhat we use protein intensities while triqler uses peptides.
@mengchun.bsky.social can you add to that?

Empirical-Bayes and Bayesian Hierarchical Modelling for Missingness and Differential Expression in Proteomics Mass spectrometry-based label-free proteomics data often suffer from missing values, especially for low-abundance proteins or when a protein is completely absent in one condition. This makes it challe...

How do you deal with missing values and "unique" proteins that were only identified in one condition in proteomics data?

Mengchun Li, an amazing PhD student in my lab, developed this great Bayesian approach. Please try it and give feedback!

www.biorxiv.org/content/10.6...

Proteomics analysis of flow cytometry-based isolated pathogen-containing phagosomes at The University of Manchester on FindAPhD.com PhD Project - Proteomics analysis of flow cytometry-based isolated pathogen-containing phagosomes at The University of Manchester, listed on FindAPhD.com

I have a PhD position available with start date September 2026 at the University of Manchester.

Proteomics analysis of flow cytometry-based isolated pathogen-containing phagosomes

Due to funding requirements, this position is for UK home students only.

www.findaphd.com/phds/project...

Nice preprint from @derm-scientist.bsky.social! Ubiquitin system is key for tissue architecture in CYLD cutaneous syndrome (CCS) skin tumours.
"Comparative ubiquitinomics of human skin reveals insulin receptor ubiquitination as a regulator of collagen secretion."
www.biorxiv.org/content/10.6...

Reposting this.

If you are interested in applying for this fellowship in a research area of our lab's interest, let me know.

Some news!

We will move to the University of Manchester @manchester.ac.uk in January!

We will keep some association with. Newcastle University for a while.

Very excited!

- as expected, quantitation at very low amounts (250 pg) is substantially worse than at "normal" loading. This will have implications on single cell proteomics.

Have a read!

4/4

- as standard for most of us, applying a 1.5-fold cut off (representing a 2-3x sigma) limits false discoveries.

- there seem to be instrument and method dependent differences in how many points per peak are necessary for good quantitation.

- be cautious with "atypical" proteomics expts where a large number of proteins change.

- the most important factor for filtering proteins to get very good quantitation is the number of quantified peptides.

- that being said, "single peptide wonders" are still surprisingly well quantified.

3/4

Using various ratios of a two and three-proteome mix enabled us to do several controlled quantitative experiments (CQEs).

They are in our experience essential to test novel DIA methods.

We identified a few recommendations such as:

2/4

Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs) Advances in mass spectrometry and associated computational tools have resulted in the wide-spread adoption of Data-Independent Acquisition (DIA) for proteomics. Experiments using state-of-the-art inst...

Are you using DIA mass spectrometry in proteomics?

We have just put this paper online: www.biorxiv.org/content/10.1...

Here, we came up with some Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)

1/4

This Friday.

Very happy that we have been awarded a £800k grant from the MRC for a novel mass spectrometer for the @newcastleuni.bsky.social NUPPA facility.
Thanks to everyone involved!

The babies born with DNA from three parents – podcast Doctors in the UK have announced the birth of eight healthy babies after performing a groundbreaking procedure that creates IVF embryos with DNA from three people. Ian Sample tells Madeleine Finlay ab...

Amazing podcast on the mitochondrial donation babies. Great work by wonderful colleagues@mitonewcastle.bsky.social at @newcastleuni.bsky.social and the @lilyfoundation.bsky.social

www.theguardian.com/science/audi...

unfortunately, I feel that the people from the latter group are the ones that shoot down grants (and papers) because in their mind we only generate "lists".

However, these lists are hugely important for communities and just because they don't appreciate them, doesn't mean they are not useful.

In life sciences there are two types of people in my experience: those that embrace and exploit omics and other large scale data technologies and those who work on one problem at the time. I had many collaborators from either side.

1/2

The financial crisis of the HE sector in the UK now leads to increased numbers of grant and fellowship applications, pushing down the success rates. Since also overheads increased, in some cases we will see success rates halved.

There is a BBSRC fellowship which will have a success rate of 5%.

@drandyfrey.bsky.social having quite some interest at his poster at #EUPA2025

We have performed a controlled quantitative experiment with a three proteome mix and come up with recommendations using DIA.

Biorxiv paper out soon (hopefully!)

The location and food will make it impossible for anyone else to ever make a better EUPA conference. Thank you for organising such an excellent event! #EUPA2025

Good morning from St. Malo.
#EUPA2025

Some of y'all can't handle 2 high agency males going at it and it really shows.

thank you!

I had expected many fewer people. Glad to see that it does not affect the conference too much!

Does anyone have an update on the number of ASMS attendees?

Woohoo, congratulations, Tanmay! Well deserved!