4 Mar 2025
Let’s talk today about Alireza Nameni, a PhD researcher at Ghent University, working at the Flanders Institute for Biotechnology @VIBLifeSciences @compomics. His research focuses on optimizing deep learning models for predicting peptide properties in proteomics
#Bioinformatics
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5 Feb 2025
De novo sequencing is transforming metaproteomics! Here's how it works & why it matters. analyticalsciencejournals.on…
@compomics @BioscienceTurku @InFLAMES_Health @UniTurku
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6 Dec 2024
Amazing talks in the second computational session #BePAc24 about missing values, CCS prediction and Proteobench, an open platform for benchmarking by @AntoninoZITO, @RobbeDevreese and Caroline Jachmann (@compomics)
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24 Nov 2024
Happy to share our immunopeptidomics pipeline using four search engine with follow-up rescoring to boost confident IDs. Also applied to timsTOF SCP data!
@ImpensLab @compomics
Preprint: biorxiv.org/content/10.1101/…
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28 Oct 2024
@RalfGabriels taking the scene to demonstrate the latest & greatest out of the @compomics group - data analytics are sure to take us where we need to be as a field! #iSCMS2024
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25 Oct 2024
A lot of talks with @compomics team and @EuBIC_ms members about #SDRF, new use cases metaproteomics, multiomics, Affinity proteomics, and how we can make easier and more accessible metadata to @pride_ebi submitters. @DeeptiJaiswal gave a great talk on the #HUPO training day.
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23 Oct 2024
Happy #HUPO2025 Wednesday!
Today from @CompOmics: @TineClaeys1's talk on tissue-specific #PTMs and posters by @RobbinBouwmees, @Pathmanaban_, and @p_verschaffelt.
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22 Oct 2024
@CompOmics Tuesday at #HUPO2024:
Join us at the @BrukerMassSpec Lunch Symposium to learn about TIMS²Rescore, at the #Bioinformatics session for Enrico's talk on modification-dependent protein associations, and checkout our posters on #MachineLearning, #Metadata & #Metaproteomics.
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21 Oct 2024
Today from @CompOmics at #HUPO2024: #metaproteomics posters, lots of initiative posters, #Bioinformatics Hub, and both @RobbeDevreese and Alireza Nameni's 3-Minute Thesis Competition.
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Thanks, Ben! I can see I’ll need some patience... My ultimate goal is to provide this option to our hospital research groups and other researchers, especially for our Hematology Clinical Department. A try to get the information translated to patients…Wish me luck!
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2 Oct 2024
I did a webinar for thermo a few years ago that has a general overview of the field and some specific info on search methods. thermofisher.com/us/en/home/…
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24 Sep 2024
On Friday the 13th (yes really), I defended my PhD at Ghent University!🎓After 4 years of diving into public proteomics, metadata and ML, I made it to the finish line! Huge thanks to my promotors @compomics , @KrisGevaert_VIB , and @juan_vizcaino for their guidance! #PhD
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6 Aug 2024
The step-by-step protocol covers sample prep, LC-MS configuration for Thunder-DDA-PASEF in timsTOF Pro, and processing in PEAKS MS2Rescore boost.
This is our SOP at @TenzerLab
And the Immunopeptidomics Platform at @HITRONMainz
@DKFZ in collaboration with @compomics lab @ugent
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29 May 2024
We combined deep-learning tools DeepLC &MS2PIP from @compomics Lab (thanks @RobbinBouwmees) and spectra properties to validate low-quality IDs. Also, we used spectrumAI from @LehtioLab (now in Python github.com/bigbio/py-pgatk/t…) to validate SAAVs #AI #deeplearning
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16 May 2024
I'm happy to announce that my junior postdoc has been funded! Excited to continue my work at @compomics together with @juan_vizcaino, diving deeper into tissue proteomics using public data and, ofcourse, pushing metadata. Grateful to @FWOVlaanderen for this opportunity!
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14 May 2024
Excited to start a new wave of blog posts---this time, highlighting new papers of PROTrEIN´s own students! We kick off with the article of @Louisebuur, in a great collaboration with @compomics started during her secondment in Ghent. Read her post here: tinyurl.com/mr33kpz9
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4 Apr 2024
Then, we teamed up with @compomics lab to integrate our IMS predictor ionmob into MS2Rescore v3 and train a timsTOF fragmentation model using HLAIp, tryptic, and elastase digest data acquired using Thunder at our lab and Carapito's lab 10.1021/acs.jproteome.3c00785 12/🧵
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18 Mar 2024
Hahaha oh Ben! missing you here. Since you asked the question, and we all know the answer 😉 let's make some time tomorrow for this. #standards and we do care for it 😎
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