Vadim Demichev
@DemichevLab
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Group Leader at @ChariteBerlin. Proteomics technologies and applications, DIA-NN author.
Berlin, Germany
Joined November 2018
With ๐๐๐-๐ก๐ก ๐ฎ.๐ฏ.๐ฌ Preview (Academia-only for now), we showcase the transformative new capabilities that have been developed in the past months. Download: https://t.co/4x5BsyVN8a
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Latest by Claudia Langenberg and her team provides insights into protein loss-of-function (LOF) mutations using three proteomics technologies within the Genes and Health cohort. This analysis focuses on the impact of complete LOF mutations on protein plasma abundance. The study
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Wrote a short perspective: Pre-trained DIA models can 'covertly' inflate FDR - and this will not show up in entrapment validation https://t.co/5xYUuP4KKI
linkedin.com
Transformer models are great? For several years, there has been this idea that one can pre-train advanced deep learning models, e.g.
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Wrote a short perspective: Pre-trained DIA models can 'covertly' inflate FDR - and this will not show up in entrapment validation https://t.co/5xYUuP4KKI
linkedin.com
Transformer models are great? For several years, there has been this idea that one can pre-train advanced deep learning models, e.g.
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Precisely mapping proteases specificity and predicting cleavage rates - with peptide libraries: https://t.co/dyc8H9Gd1B. This is a powerful application that is uniquely enabled by the peptidoform confidence and QuantUMS modules in DIA-NN 2.0.
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Youโre still able to join us at #AMC2025! Due to high demand we opened a few more seatsโฆwe are looking forward to great discussions on host-microbiome and aging!
#AMC2025 is almost here (Oct 28โ29, Jena) and weโve opened a few more seats! If you work on host-microbiome interactions, aging, or age-related diseases, bring a poster and join this amazing crowd! โจ Highlights ๐ฃ๏ธ Keynotes: Karine Clรฉment, Niranjan Nagarajan (online), Gianni
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I will be at the ๐๐๐-๐๐ session @ ๐๐ก๐๐ซ๐ฆ๐จ ๐๐ซ๐จ๐ญ๐๐จ๐ฆ๐ ๐๐ข๐ฌ๐๐จ๐ฏ๐๐ซ๐๐ซ & ๐๐จ๐ฆ๐ฉ๐จ๐ฎ๐ง๐ ๐๐ข๐ฌ๐๐จ๐ฏ๐๐ซ๐๐ซ User Meetings in Bremen, Germany, ๐-๐๐ ๐๐๐๐๐ฆ๐๐๐ซ. With some cool advances for DIA-NN on Thermo instruments.
thermofisher.com
Proteome Discoverer & Compound Discoverer Users Meeting, Real-world case studies, cutting-edge workflows, and practical insights from Thermo Fisher Scientific experts and fellow users to help you...
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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
linkedin.com
With ๐๐๐-๐ก๐ก ๐ฎ.๐ฏ.๐ฌ Preview (Academia-only for now), we showcase the transformative new capabilities that have been developed in the past months. Download: https://lnkd.in/ehFF2Mf4, release...
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Out now in @CellSystemsCP: Deep Visual Proteomics shows xenotransplantation drives colon #organoids toward in-vivo-like proteomes supporting their use in regenerative medicine; culture tweaks can mimic this shift. With @JensenLab_UCPH. Frederik Post @Freddyomics explains further:
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Chemoproteomics: can we trust the search engine? Since inception of DIA-NN, we always prioritised data quality. A nice benchmark by Ana Martinez del Val and colleagues: https://t.co/agQzJ3rzhP Paper: https://t.co/EYcvPxxJmT (for benchmark: see supplementary figure S2)
pubs.acs.org
Oxidative damage plays a critical role in various diseases including cardiovascular and neurological disorders. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure...
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We have updated our Slice-PASEF preprint! It's a result of a large collaboration where we highlight its advantages for single cell proteomics. Or any other applications benefiting from sensitivity. For example, major gains for ubiquitinomics:
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Dear colleagues, would you like DIA-NN interface to change or stay similar? Would be grateful if you reply with your thoughts on this. The rationale behind the current interface is to enable quick work with multiple experiments, helped by: - Multiple independent tabs. - All
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An exciting new paper proteomics paper describes novel insights on protein-disease mechanisms by using @seer-based MS combined with genomic data on the Genes & Health cohort. From the abstract by Maik Peitzner, Claudia Langenberg and colleagues: "... we idenIfy >1,200
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Proteostasis and Unfolded Protein Response Dynamics in Human Neuron and Mouse Glia Co-culture Reveal Cell-Specific Aging Responses https://t.co/FmnL7fcIgs
#biorxiv_biochem
biorxiv.org
Proteostasis, or protein homeostasis, is a tightly regulated network of cellular pathways essential for maintaining proper protein folding, trafficking, and degradation. Neurons are particularly...
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DNA copy number variation is strongly buffered at the protein level. The buffering is much stronger than at the RNA level.
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A fully automated plasma #proteomics workflowโspanning prep to #Evotip loadingโusing #Evosep One + #Biomek i5 is enabling scalable, cost-efficient clinical research. Explore how #automation meets reproducibility in our latest blog post: https://t.co/plUosXEOFM
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