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Matthias Trost @mtrost.bsky.social · 2d

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!

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Matthias Trost @mtrost.bsky.social · 15d

- 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!

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Matthias Trost @mtrost.bsky.social · 15d

- 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.

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Matthias Trost @mtrost.bsky.social · 15d

- 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.

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Matthias Trost @mtrost.bsky.social · 15d

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:

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Matthias Trost @mtrost.bsky.social · 15d

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)

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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...

eur03.safelinks.protection.outlook.com

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Matthias Trost @mtrost.bsky.social · Jul 27

This Friday.

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Matthias Trost @mtrost.bsky.social · Jul 26

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!

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Matthias Trost @mtrost.bsky.social · Jul 22

Amazing podcast on the mitochondrial donation babies. Great work by wonderful [email protected] at @newcastleuni.bsky.social and the @lilyfoundation.bsky.social

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

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...

www.theguardian.com

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Matthias Trost @mtrost.bsky.social · Jun 27

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.

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Matthias Trost @mtrost.bsky.social · Jun 27

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.

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Matthias Trost @mtrost.bsky.social · Jun 20

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%.

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Matthias Trost @mtrost.bsky.social · Jun 19

@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!)

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Matthias Trost @mtrost.bsky.social · Jun 19

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

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Matthias Trost @mtrost.bsky.social · Jun 17

Good morning from St. Malo.
#EUPA2025

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Matthias Trost @mtrost.bsky.social · Jun 6

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

Matthias Trost @mtrost.bsky.social · Jun 6

thank you!

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

Matthias Trost @mtrost.bsky.social · Jun 6

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

Matthias Trost @mtrost.bsky.social · Jun 2

Does anyone know how many delegates are at #ASMS2025 ?

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

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Matthias Trost @mtrost.bsky.social · Jun 5

Woohoo, congratulations, Tanmay! Well deserved!

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Reposted by Matthias Trost

Ada Palmer @adapalmer.bsky.social · Jun 3

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.

Benjamin Dreyer @bcdreyer.social · Jun 3

This is a hell of a thing to read.

Diabolus Ex Machina

This Is Not An Essay

open.substack.com

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Matthias Trost @mtrost.bsky.social · Jun 2

Does anyone know how many delegates are at #ASMS2025 ?

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

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Matthias Trost @mtrost.bsky.social · May 28

Interesting! Any news on the new Bruker kit?

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Matthias Trost @mtrost.bsky.social · May 16

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)

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Reposted by Matthias Trost

Ed Emmott @edemmott.bsky.social · May 14

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

Ed Emmott @edemmott.bsky.social · May 11

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...

Annual Meetings | BSPR

www.bspr.org

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Reposted by Matthias Trost

Ed Emmott @edemmott.bsky.social · May 11

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...

Annual Meetings | BSPR

www.bspr.org

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