Matthias Trost

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!

Wow, yes. An amazing glimpse of the LLM Lie Machine at work. Anyone whose students are bring tempted by LLMs, sharing this could be very helpful showing how it lies, and how it fails.

Does anyone know how many delegates are at #ASMS2025 ?

I would assume that immigration policy and the blocking of grants will affect the numbers...

Interesting! Any news on the new Bruker kit?

Show the ratios of all peptides of the protein.

If you have plenty of peptides, and replicates, this can be very convincing.

If it is a protein quantified on few peptides, a WB may make sense.

(Although we recently tested our pipeline and even single hit wonders are amazingly well quantified)

Two days left for abstract submission and early bird registration for BSPR2025!

Less than one week to go until the deadline for abstract submission and early bird registration for the British Society for Proteome Research @ukbspr.bsky.social annual conference 2025 in Liverpool! Deadline is Friday May 16! For more details see here: www.bspr.org/annual-meeti...

Who would have thought that hard right nationalist governments do ethnic cleansing and start wars?

Labour dropping Net Zero will lead to Reform voters still voting Reform and Labour voters voting for the Greens.

God, show some spine and do what is right.

Sigh. Want to go to two conferences in France and ideally take the train to reduce my CO2 output.

To get to Paris I can either spend £500 to take the train or fly for £88.

This is so fucked up.

Flow cytometry-based isolation combined with ultra-sensitive proteomics of Salmonella-containing phagosomes reveals novel insights into host-pathogen interactions Macrophages engulf pathogens into dynamic phagosomes, which many bacteria manipulate for survival. However, isolating pure pathogen-containing phagosomes remains challenging. Here, we developed a nove...

I would like to share our latest work: After years of optimisation, we have developed a flow cytometry-based method to isolate pathogen-containing phagosomes. Paired with sensitive proteomics, this provides exciting new insights into host-pathogen interactions!

www.biorxiv.org/content/10.1...