Matthias Trost

Matthias Trost

@mtrost.bsky.social

Professor of Proteomics. Currently at Newcastle University UK. he/him Here in personal capacity.

1.9K followers1.9K following165 posts

Matthias Trost reposted

Benjamin Raymond
@drbenraymond.bsky.social

So happy to have this work out and to continue applying our cutting-edge mass spectrometry approaches to study the clearance of apoptotic cells by #Macrophages.

Matthias Trost@mtrost.bsky.social

New paper from our lab. Driven by Ben Raymond, who now is a BBSRC fellow and builds his own line of research on this paper. Ben developed a method to define the proteome of macrophages after uptake of SILAC-labelled apoptotic cells. 1/2 www.nature.com/articles/s41...

nature.comEfferocytosis triggered proteomic reprogramming of macrophages reveals CD97 as a novel apoptotic receptor - Cell Death & DifferentiationCell Death & Differentiation - Efferocytosis triggered proteomic reprogramming of macrophages reveals CD97 as a novel apoptotic receptor
Matthias Trost
@mtrost.bsky.social

New paper from our lab. Driven by Ben Raymond, who now is a BBSRC fellow and builds his own line of research on this paper. Ben developed a method to define the proteome of macrophages after uptake of SILAC-labelled apoptotic cells. 1/2 www.nature.com/articles/s41...

nature.comEfferocytosis triggered proteomic reprogramming of macrophages reveals CD97 as a novel apoptotic receptor - Cell Death & DifferentiationCell Death & Differentiation - Efferocytosis triggered proteomic reprogramming of macrophages reveals CD97 as a novel apoptotic receptor
Matthias Trost
@mtrost.bsky.social

Macrophages are reprogrammed after uptake of apoptotic cells and induce CD97 which he then shows is a apoptotic receptor. This is evolutionary conserved from fly, to mouse and human. 2/2

Matthias Trost
@mtrost.bsky.social

We have a 2-year postdoc position available for a bacterial infection biologist. We will use our exciting PhagoCyt method which uses flow cytometry to isolate pathogen-containing phagosomes & sensitive proteomics. Research Associate at The University of Manchester www.jobs.ac.uk/job/DSK144/r...

jobs.ac.ukResearch Associate at The University of ManchesterExplore an exciting academic career as a Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
Matthias Trost
@mtrost.bsky.social

If you need another reason to use proteomics to quantify proteins rather than Western Blot:

Reese Richardson@reeserichardson.bsky.social

The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)

Matthias Trost
@mtrost.bsky.social

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...

share.googleWill 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 ...
Matthias Trost
@mtrost.bsky.social

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...

jobs.manchester.ac.ukResearch Associate:Oxford RoadThe successful candidate would be expected to be curious and rigorous, with demonstrable knowledge of cell biology relevant to the research focus of the laboratory and substantial hands-on experience with mass spectrometry platforms.
Matthias Trost
@mtrost.bsky.social

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...

biorxiv.orgEmpirical-Bayes and Bayesian Hierarchical Modelling for Missingness and Differential Expression in ProteomicsMass 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...
Matthias Trost
@mtrost.bsky.social

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...

findaphd.comProteomics analysis of flow cytometry-based isolated pathogen-containing phagosomes at The University of Manchester on FindAPhD.comPhD Project - Proteomics analysis of flow cytometry-based isolated pathogen-containing phagosomes at The University of Manchester, listed on FindAPhD.com
Matthias Trost
@mtrost.bsky.social

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

Michael Brockhurst@brockhurstlab.bsky.social

Three Bicentenary research fellowships on offer at @officialuom.bsky.social @fbmh-uom.bsky.social for exceptional ECRs with <3y postdoc experience 3yrs salary + £30k pa research expenses Do you have a great idea & want to join @mermanchester.bsky.social? www.bmh.manchester.ac.uk/research/sup...

bmh.manchester.ac.ukBicentenary Early Career Research Fellowships | Biology, Medicine and Health | University of ManchesterFind out about and apply for a Bicentenary Early Career Research Fellowship.
Matthias Trost
@mtrost.bsky.social

- 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.

Matthias Trost
@mtrost.bsky.social

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

Matthias Trost
@mtrost.bsky.social

- 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

Matthias Trost
@mtrost.bsky.social

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...

theguardian.comThe babies born with DNA from three parents – podcastDoctors 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...
Matthias Trost
@mtrost.bsky.social

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

Matthias Trost
@mtrost.bsky.social

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.

Matthias Trost
@mtrost.bsky.social

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%.

Matthias Trost reposted

Ed Emmott
@edemmott.bsky.social

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

Ed Emmott@edemmott.bsky.social

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...

bspr.orgAnnual Meetings | BSPR
Matthias Trost
@mtrost.bsky.social

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.

Zoë Crowther@zoecrowther.bsky.social

Labour MPs are starting to get nervous about net zero, after a disappointing set of election results A minister cast doubt over Ed Miliband's political future An MP said net zero could "play out the same way as Brexit" Story by me & @matildamartin.bsky.social 👇

politicshome.comLabour Figures Starting To Get Nervous About Net Zero Following Local Election ResultsLabour MPs are growing increasingly nervous about the government’s approach to net zero following Reform’s sweeping success in the local and mayora...
Matthias Trost
@mtrost.bsky.social

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.

Matthias Trost
@mtrost.bsky.social

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...

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