Lightnews — Scholar-powered news

Reposted by MaP-Proteomique

Vadim Demichev @vadim-demichev.bsky.social · 7d

I will be at the 𝐃𝐈𝐀-𝐍𝐍 session @ 𝐓𝐡𝐞𝐫𝐦𝐨 𝐏𝐫𝐨𝐭𝐞𝐨𝐦𝐞 𝐃𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐞𝐫 & 𝐂𝐨𝐦𝐩𝐨𝐮𝐧𝐝 𝐃𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐞𝐫 User Meetings in Bremen, Germany, 𝟗-𝟏𝟏 𝐃𝐞𝐜𝐞𝐦𝐛𝐞𝐫. With some cool advances for DIA-NN on Thermo instruments. www.thermofisher.com/de/de/home/e...

This link will take you to a page that’s not on LinkedIn

lnkd.in

1 7

Reposted by MaP-Proteomique

MaP-Proteomique @map-proteomique.bsky.social · 6d

Great to welcome Sébastien JeanJean, Senior Sales Manager France at @thermofishersci.bsky.social, to visit our new #OrbitrapAstral mass spectrometer installation today!
Big thanks to our funders — CPER, LNCC, @ibisa.net, Amidex, and @inserm.fr.
#MassSpec #Proteomics @insermpacacorse.bsky.social

4 5

MaP-Proteomique @map-proteomique.bsky.social · 6d

Great to welcome Sébastien JeanJean, Senior Sales Manager France at @thermofishersci.bsky.social, to visit our new #OrbitrapAstral mass spectrometer installation today!
Big thanks to our funders — CPER, LNCC, @ibisa.net, Amidex, and @inserm.fr.
#MassSpec #Proteomics @insermpacacorse.bsky.social

4 5

Reposted by MaP-Proteomique

Vadim Demichev @vadim-demichev.bsky.social · 9d

In DIA-NN 2.3.0, we have added Deamidation (NQ) as an option in the GUI. There are good reasons for it :) You can try InfinDIA with any number of modifications selected, and check the RT differences between modified vs respective stripped peptides, for each mod - a way to validate peptidoform FDR.

2 12

Reposted by MaP-Proteomique

Vadim Demichev @vadim-demichev.bsky.social · 12d

With 𝗗𝗜𝗔-𝗡𝗡 𝟮.𝟯.𝟬 Preview (Academia-only for now), we showcase the transformative new capabilities that have been developed in the past months. Download: github.com/vdemichev/Di...

3 4 27

Reposted by MaP-Proteomique

ReSyn Biosciences @resynbio.bsky.social · 15d

🚨Publication alert🌶️: #Immunopeptidomics is a trending for good reason! A team from @ki.se identify ovarian tumor-derived peptide that induces memory-like features in natural killer cells, paving the way for new cancer immunotherapy strategies! www.biorxiv.org/content/10.1...

Recognition of Ovarian Tumor-Derived Non-canonical Peptide Induces Memory-Like Features in Natural Killer Cells

Immune cell-based immunotherapy has emerged as a promising strategy for both hematologic malignancies and solid tumors. The adaptive properties of T and B cells, namely, antigen specificity and long-t...

www.biorxiv.org

1 3

Reposted by MaP-Proteomique

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)

1/4

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...

eur03.safelinks.protection.outlook.com

2 9 29

Reposted by MaP-Proteomique

Michael MacCoss @maccoss.bsky.social · 23d

Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...

#massspec #proteomics

Start Page: /home/software/Skyline/events/2025 Webinars/Webinar 26

skyline.ms

16 31

Reposted by MaP-Proteomique

IonOpticks @ionopticks.bsky.social · 23d

@kentsisresearch.bsky.social develop a proteogenomics workflow to detect 1000s of unknown cancer proteins. PG3 combines long-read RNA sequencing with multi-protease MS to discover non-canonical proteins in cancer cells. Used a timsTOF HT, nanoElute 2 & Aurora Ultimate 25x75 column:
bit.ly/4mlQSmu

3 10

Reposted by MaP-Proteomique

Nikolai Slavov @slavov-n.bsky.social · Aug 28

The key molecules in immune responses are glycoproteins.

Why isn't glycosylation studied more intensively?

It should be.
It's a challenging research area, but a good one for ambitious & audacious scientists.

2 4 22

Reposted by MaP-Proteomique

Vadim Demichev @vadim-demichev.bsky.social · Jul 25

Time and time again, it's always the same picture. DIA-NN controls FDR correctly as data reliability has been the main goal at DIA-NN's conception back in 2017 and a priority since then.

1 5 14

MaP-Proteomique @map-proteomique.bsky.social · Jul 23

In fact, two essential companions were installed: the Evosep ENO @evosep.bsky.social and the Ionbench table #IonBench

MaP-Proteomique @map-proteomique.bsky.social · Jul 23

A new companion for our mass spectrometer.

2 3

MaP-Proteomique @map-proteomique.bsky.social · Jul 23

A new companion for our mass spectrometer.

1

Reposted by MaP-Proteomique

J.-F. Cavalier @jefcavalier.bsky.social · Jun 25

Today is a great day!
Our article accepted on March 19, 2025 is published in Wiley mLife journal.
Great collaborative work with JM Bolla's lab, @map-proteomique.bsky.social @canaanlab.bsky.social
Céline Crauste from @ibmm-balard.bsky.social, and more...

👉 onlinelibrary.wiley.com/doi/10.1002/...

The polyamino‐isoprenyl enhancer NV716 enables the antibacterial activity of two families of multi‐target inhibitors against the ESKAPEE bacterium Enterobacter cloacae

Gram-negative bacteria are particularly prone to developing antimicrobial resistance (AMR), as evidenced by the WHO's ESKAPEE list of high-priority pathogens. One strategy that has increased is the u...

onlinelibrary.wiley.com

3 6

MaP-Proteomique @map-proteomique.bsky.social · Jun 20

At the European Proteomics Congress in St Malo #EuPA2025, Marseille Proteomique @map-proteomique.bsky.social won 3rd prize in the sandcastle competition sponsored by @brukercorporation.bsky.social

2 8

Reposted by MaP-Proteomique

CompOmics @compomics.com · Jun 16

From PTMs to proteins, from metadata to metaproteomics. CompOmics has got you covered at #EuPA2025!

Plenary talk

Lennart Martens
Rise of the Robots – definitely artificial, somewhat intelligent

Keynote lecture

Tim Van Den Bossche
Improving metaproteomics data analysis with the Ghent Metaproteomics Toolbox

Oral presentations

Harikrishnan Ramadasan
Bridging expert curation and LLMs for automated metadata extraction in lesSDRF 2.0

Robbe Devreese
Collisional cross-section prediction for peptides and small molecules: covering all bases (and bridging the gap?)

Robbin Bouwmeester
Challenges and opportunities in modification searches for DIA proteomics

Educational session

Lennart Martens
No more surprises: AI predictions in MS DDA and DIA data interpretation

Robbin Bouwmeester
A deep dive into limitations of modification searching for DIA data

Caroline Jachmann
Fantastic PTMs and how (not?) to find them using msqrob2PTM -
a real-life journey

Poster presentations

Enrico Massignani
Overcoming challenges in non-canonical protein searches with OpenProt and ionbot

Pathmanaban Ramasamy
Assessing the relation between protein phosphorylation, AlphaFold3 models and conformational variability

Toon Callens
Advancing tissue prediction using read-based DNA methylation modelling towards a multi-omics integration

Tine Claeys
MLMarker: Data-driven discovery of tissue similarity and biomarkers

Alireza Nameni
Enhancing peptide-spectrum match identification with non-linear models in Mokapot: Assessing complexity, overfitting, and false discovery rates

Tim Van Den Bossche
The Metaproteomics Initiative: An international community by and for metaproteomics researchers

Award presentations

Tine Claeys
Bioinformatics Award

Tim Van Den Bossche
Vision & Commitment Award

8 22

MaP-Proteomique @map-proteomique.bsky.social · Jun 16

On the way to the European #proteomics association #EuPA2025 conference in St Malo

1 3

MaP-Proteomique @map-proteomique.bsky.social · Jun 3

Our new mass spectrometer has come to life. Now we're going to have to feed it protein several times a day.

1 4

MaP-Proteomique @map-proteomique.bsky.social · May 23

Marseille Proteomics @map-proteomique.bsky.social begins is delighted to announce that our new spectrometer is now out of the box and will start running next week

2 2

Reposted by MaP-Proteomique

MaP-Proteomique @map-proteomique.bsky.social · May 23

A new era for Marseille Proteomics have just reached 100 subscribers to @map-proteomique.bsky.social begins with the arrival of these boxes containing new generations of equipment.

2 2

MaP-Proteomique @map-proteomique.bsky.social · May 23

A new era for Marseille Proteomics have just reached 100 subscribers to @map-proteomique.bsky.social begins with the arrival of these boxes containing new generations of equipment.

2 2

Reposted by MaP-Proteomique

Impens Lab @impenslab.bsky.social · May 16

🚨 New preprint! 🚨
Presenting diaPASEF immunopeptidomics for bacterial epitope discovery.
💥 Showcasing DIA-NN immunopeptidomics using proteome-wide predicted HLA class I libraries!
🧬 Read more: biorxiv.org/cgi/content/...
#Immunopeptidomics #MassSpec #DIA #HLA

Data-independent immunopeptidomics discovery of low-abundant bacterial epitopes

Mass spectrometry-based immunopeptidomics is a powerful approach to uncover peptides presented by human leukocyte antigen (HLA) molecules that can guide vaccine design and immunotherapies. While data-...

biorxiv.org

8 22

Reposted by MaP-Proteomique

Evosep @evosep.bsky.social · May 4

May the 4th be with you! Celebrate Star Wars Day with the force of Evotip Pure, the trusted ally for your LC-MS journeys!

#MayThe4th #StarWarsDay #LCMS

1 2

Reposted by MaP-Proteomique

Alexey Nesvizhskii @nesvilab.bsky.social · May 5

Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!

4 15 77

Reposted by MaP-Proteomique

MaP-Proteomique @map-proteomique.bsky.social · May 3

Marseille proteomics joins #starwars Day to explore the universe of the proteome on a new dimension. May the fourth be with you

2 4