Friday, May 6, 2022

What happened at EUPA 2022?? -- Guest blog post special!

I have been buried in work linked to maintaining my employment for several weeks. So buried that I scheduled a lot of blogposts for 2032. I'll leave them there so they'll post again later.

The annual congress of EuPA is something I've always wanted to attend and it has never quite worked out, so I conned some guest bloggers into providing some insight about what happened at the conference. (Sorry for the month long delay). 

At Proteomics Forum/EuPA2022 in Leipzig, we got word of the shout out from across the ocean to provide a little update on the most exciting stuff that was presented. In search of a brief format, Ghent attendees (#GhentRepresent) spread out and each of us came up with a personal perspective on the most exciting stuff, a predominantly ECR perspective:


Arthur Declercq:EuPA2022 was the conference of tackling problems in specific proteomics niches such as single cell or immunopeptidomics. It was very nice the see many people showed up for the immunoproteomics symposium where Michal Bassani-Sternberg gave her talk about identifying neo-epitopes for personalized cancer immunotherapy with their proteogenomics pipeline NeoDisc, showing how they bring state-of-the-art research from bench to bedside (10.1038/s41587-021-01072-6).

Ben commentary: Hey! This is one of the two immunopeptidomics splicing groups!  Despite the controversy about whether HLA peptides splice or not, there are some very successful clinical trials going on right now centered on weird spliced peptides. 


Tine Claeys: “The diversity of proteomics and its wide variety of instrument, tools, applications, … shows the creativity of scientist in tackling very different problems. I was intrigued by the talk from Jennifer Van Eyk on how her group approaches clinical applications and biomarker discovery integrating multi-omics analyses. Combining already existing clinical data with the new advancements in the mass spec field to determine your molecular twin demonstrated again the importance of big-data analysis, especially in a clinical context.  The talk from Ileana Cristea on spatiotemporal organelle remodeling ( 10.1016/j.celrep.2020.107943) blew my mind on how the location of a protein can have a huge impact and can be very altered upon viral infection but we're still mainly focused on protein abundance. This will definitely impact the way I approach my own research. I've had some amazing interactions with amazing people and expanded my scientific horizon in ways that would've been impossible without Proteomics Forum 2022!”


Toon Callens: “As I just started my PhD in proteomics (bioinformatics) it was great to see what everyone is working on and to have a broad overview of the field and the state-of-the-art. It was also interesting to see overlap with my own projects, which gave me some new ideas.”


Annelies Bogaert:Single cells, single cells, single cells! It is great to see how much progress has been made in this field. Also great to see how proteomics is contributing to help conquer the covid-19 pandemic. Chris Overall his talk about how they used TAILS to identify substrates of the SARS-CoV-2 3CLpro protease which gives insights in how the virus uses this to its benefit, is just one great example (10.1016/j.celrep.2021.109892). While Albert Heck gave a nice presentation showing that we are evolving to personalized diagnostic as top down comparisons of IgG antibodies from one person over time could in the future help diagnose medical conditions (10.1016/j.cels.2021.08.008). Since I spend some of my time trying to understand better the functionality of proteoforms (thanks to Neil Kelleher for introducing this term [10.1038/nmeth.2369]) it was nice to hear that so many talks also considered them and stressed their importance as they are often still neglected! And as a last note, this conference really showed that DIA is becoming the standard over DDA.”


Tim Van Den Bossche: “I was really honored to present the flagship manuscript of the Metaproteomics Initiative and give a short introduction about the Initiative itself. Where the field 10 years ago was often overlooked, it's amazing to see that there's now a dedicated metaproteomics session at the major European proteomics conference”

 Ben commentary: This is the metaproteomics initiative mentioned:

Ralf Gabriels: “Proteomics is done with simple setups; more challenging workflows is where the interest is now: Single cell, subcellular/spatial, immunopeptidomics, metaproteomics, proteogenomics, open modification... And quantification labels are coming to DIA!? Both non-isobaric with plexDIA (10.1101/2021.11.03.467007) and isobaric with DIA-TMT (10.1016/j.mcpro.2021.100177).”

Ben commentary: 

 Maarten Dhaenens: “plexDIA, using 3-plex nonisobaric mass tags: how could I have missed this one? (Nikolai Slavov) (10.1101/2021.11.03.467007)

Neil Kelleher is doing stuff with single ions I will never understand because I am a QTOF person, but he is so right that “we should measure what we must, not what we can!”. 

Markus Ralsner suggested ordering your differential proteins according to chromosome localization, because you might in fact be looking at an aneuploidy event in your cell lines. That reminds me of a shrimp project where we once were thinking along the same lines, but we never really showed it as beautifully as Markus did! 

And OMG, Kathryn Lilley is leaving us to look at nucleotide biomolecules?! Nooooooooo! But then again: what she is noticing on subcellular RNA localization is beyond cool. Please Kathryn, come back when you finished throwing over their world view and throw over ours a few more times?  

Vadim Demichev got across the message that Match Between Runs (MBR) is making a significant difference in the current DIA-NN implementation. Therefore, he does upfront peak picking and alignment. And hey, that reminded me of something we were doing a while ago... 

In fact, just talking about it became the biggest breakthrough for me personally: our ion-networks could finally be revived (10.1101/726273), all because of the return of in-person interactions and how these are so different from digital meetings! I am convinced that Bruker data will turn out to be the perfect match for ion-networks. So, if ion-networks are a “sleeping beauty”, then Proteomics Forum/EuPA2022 sure woke her up!”

Ben commentary: whoa....check out the highlighted stuff....this happens all the time in cancer, particularly when cells are treated with platinum based therapies. Worth considering, for real...

Lennart Martens: “Lots of great interactions and creative new ideas at the first in-person meeting in ages. Also… CAKE!”

Ben commentary: Wait. THE Lennart Martens? Holy shit... This was a great idea! 

CONCLUSION: The conference hall was part of the Zoo of Leipzig. After the conference, we visited the zoo and found a fish that perfectly illustrated how our heads felt after a full week of in-person conference!


Guest reporters:

Arthur Declercq (@DeclercqArthur) 1,3
Tine Claeys (
@TineClaeys1) 1,3
Toon Callens (
@ToonCallens) 1,3
Annelies Bogaert (
@AnneliesBogaert) 2,3
Tim Van Den Bossche (
@tvdbossche) 1,3
Ralf Gabriels (
@RalfGabriels) 1,3
Maarten Dhaenens (
@MaartenDhaenens) 4
Lennart Martens (
@CompOmics) 1,3

1. CompOmics, VIB-UGent Center for Biotechnology, VIB, Ghent, Belgium
2. Gevaert Lab, VIB-UGent Center for Biotechnology, VIB, Ghent, Belgium
3. Department of Biomolecular Medicine, Ghent University, Belgium
4. ProGenTomics, Department of Pharmaceutics, Ghent University, Belgium

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