Very excited to present my poster about #MS2Rescore and open modification immunopeptidomics searches at #ASMS2023! Interested? Come see me at posterboard ThP 375, see ya there!
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Arthur Declercq
23 posts
Arthur Declercq
@DeclercqArthur
PhD student at @CompOmics (VIB-UGent), @VIBLifeSciences Bioinformatics | Machine learning | Immunopeptidomics
Katılım Haziran 2014
130 Takip Edilen162 Takipçiler
Arthur Declercq retweetledi
Presenting my (wrinkly) poster on lesSDRF at #ELIXIR23 🤗 Come by if you want to know how to annotate your #proteomics data without any hassle, and get your #metadata easily in SDRF format.
Not in the neighbourhood? You can read our preprint here: researchsquare.com/article/rs-293…
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Arthur Declercq retweetledi
The new and updated models of MS2pip core library show greatly improved peptide identifications in #immunopeptidomics!
academic.oup.com/nar/advance-ar…
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Arthur Declercq retweetledi
DeepLC now supports psm_utils. So no more parsing of the input file! Works directly on msms.txt, idXML, mzIdentML, and many more file formats.
Transfer learning is now available in the GUI and python library on PyPI.
See the latest release here:
github.com/compomics/Deep…
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Exciting news! Our latest publication on MS²PIP is now available in the Nucleic Acid Research web server issue. Check it out here doi.org/10.1093/nar/gk… or go directly to iomics.ugent.be/ms2pip/ to check out the new features 🚀 #CompOmics #NucleicAcidResearch #MS2PIP
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Arthur Declercq retweetledi
As a spin-off from MS²Rescore, we developed psm_utils: a Python package to read and write various PSM file formats and to handle peptidoforms, PSMs, and PSM lists through a user-friendly and high-level API.
Docs: psm-utils.readthedocs.io
Preprint: doi.org/10.26434/chemr…
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Arthur Declercq retweetledi
MS2Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates | buff.ly/3NOfO4U #proteomics
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I'm very excited to announce my research paper on boosting immunopeptide identification rates with MS²Rescore is in press at @molcellprot ! Go check it out at doi.org/10.1016/j.mcpr…
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I'm very excited to be amongst the guest speakers for the upcoming EPIC-XS computational proteomics event.
EPIC-XS@epic_xs
It really is free and less than 2 weeks away. Register now for the EuPA and EPIC-XS workshop and webinar on Computational Proteomics compomics.com/events/2022-ep…
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Arthur Declercq retweetledi
Mass spec software is all good, but have you even felt the intensity of your peaks? (x-axis=retention time, y-axis=MS1 m/z, z-axis= intensity) From now on I will only inspect my data after 3D printing it first ;)
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Proud to present my poster p201 abstract 230) on greatly improving #immunopeptidomics identifications at #EuPA2022
Come have a chat on 06/04 in the Händel room during the poster session!
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Arthur Declercq retweetledi
Everyone ready for an exciting @EuPAProteomics conference in #Leipzig? Here's an overview of the Ghent delegation at #EuPA2022:
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Arthur Declercq retweetledi
The last CompOmics group meeting of 2021 went a bit... meta. Yes, this is the real deal: 11 pioneering group members are having a VR group meeting in Horizon Workrooms. Amazing technology; this is a game changer! While we're working from home, all our meetings will be here.
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Excited to present our work on #immunopeptidomics rescoring with MS²Rescore at #HUPOReCONNECT 2021 poster presentation (P11.09) today at 16:00 UTC
CompOmics@compomics
Here's an overview of @CompOmics at #HUPOReCONNECT 2021. Checkout out posters today at 16:00 UTC, Sven's talk on #ionbot Friday at 0:55 UTC, and the session "The Future of Proteomics" Lennart is chairing with @mlaval6, also on Friday.
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@DavidGomezZep @RobbinBouwmees Hi @DavidGomezZep, thanks for the interest! We are aware of the increased use of PEAKS in immunopeptidomics and are already working on implementing it. It should be available in the near future! Keep an eye on the github.com/compomics/ms2r…!
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@RobbinBouwmees This looks great! I didn't see PEAKS in the accepted output files. Are planning to make it compatible? A lot of people in the immunopeptidomics community use it; although it is proprietary
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Crucial part of this research are the predictions from (retrained) MS²PIP and DeepLC for rescoring PSMs.
I actually did not expect the tryptic trained models in DeepLC to show high accuracy on non-tryptic peptides. It is always fun to push model generalizibility to the edge!
CompOmics@compomics
Manuscript on our top performing immunopeptidomics identification engine now out in bioRxiv: biorxiv.org/content/10.110… - if you are interested in 30% more unique identified immunopeptides, or if you care about top performance even at 0.1% FDR (!!), then definitely check it out!
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Arthur Declercq retweetledi
MS²Rescore is available at github.com/compomics/ms2r…. Try it out, and let us know what you think. Feature requests are always welcome!
New #immunopeptidomics models coming online very soon, GUI and Windows support are in the works.
CompOmics@compomics
Manuscript on our top performing immunopeptidomics identification engine now out in bioRxiv: biorxiv.org/content/10.110… - if you are interested in 30% more unique identified immunopeptides, or if you care about top performance even at 0.1% FDR (!!), then definitely check it out!
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The word is out! Check out our immunopeptidomics rescoring tool at github.com/compomics/ms2r… or read all about it on bioRxiv biorxiv.org/content/10.110….
CompOmics@compomics
Manuscript on our top performing immunopeptidomics identification engine now out in bioRxiv: biorxiv.org/content/10.110… - if you are interested in 30% more unique identified immunopeptides, or if you care about top performance even at 0.1% FDR (!!), then definitely check it out!
English