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Tatiana Shamorkina

@tshamorkina.bsky.social
399 followers 879 following 2 posts

Proteomics facility manager at A. Hecklab, Utrecht University; PhD candidate @Snijderlab with interest in microbs and host interactions

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Reposted by Tatiana Shamorkina
Joost Snijder @joostsnijder.bsky.social · 09/04/2026
Out now at PLoS Pathogens @plos.org. Nice collaboration with @danielhurdiss.bsky.social @utrechtvirology.bsky.social. Some beautiful glycoproteomics work by @tshamorkina.bsky.social mapping N- and O-glycan shield of coronaviruses infecting whales and dolphins 🐋🐬🐳. journals.plos.org/plospathogen...
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Reposted by Tatiana Shamorkina
Joost Snijder @joostsnijder.bsky.social · 30/03/2026
Host cell remodeling via cyclin dependent kinases drives Ebola virus replication and transcription. www.biorxiv.org/content/10.6... Check out our latest preprint. Great work by @tshamorkina.bsky.social. Thanks to co-authors Danni Snikkers and @hecklab.bsky.social
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Reposted by Tatiana Shamorkina
Joost Snijder @joostsnijder.bsky.social · 23/03/2026
We did a plasma proteomics study on dengue disease severity in children with Tineke Cantaert and identified early markers of endothelial and inflammatory activation. Great work by @tshamorkina.bsky.social and Sofia! Thanks to all co-authors @hecklab.bsky.social. www.medrxiv.org/content/10.6...
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Reposted by Tatiana Shamorkina
Joost Snijder @joostsnijder.bsky.social · 11/03/2026
These HTA proteases from archaea work great for mass spec-based antibody sequencing. Paper out now in final form at Cell Systems. Congrats to @tshamorkina.bsky.social @tkadava.bsky.social @lperezpaneda.bsky.social and @hecklab.bsky.social www.sciencedirect.com/science/arti...
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Joost Snijder @joostsnijder.bsky.social · 01/06/2025
Go find Tatiana Shamorkina, Douwe Schulte, and Weiwei Peng at ASMS this year. They've been very busy with their antibody sequencing work and would love to chat! @tshamorkina.bsky.social
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Tatiana Shamorkina @tshamorkina.bsky.social · 30/05/2025
We are excited to have it out: a combination of archaeal proteases and hybrid fragmentation for antibody de novo sequencing. Poster TP-005 #asms2025 #teammassspec It was a true team effort @lperezpaneda.bsky.social @tkadava.bsky.social @joostsnijder.bsky.social and @hecklab.bsky.social
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Reposted by Tatiana Shamorkina
Laura Pérez @lperezpaneda.bsky.social · 29/05/2025
Excited to share our new preprint on archaeal proteases boosting reads in de novo antibody sequencing! Team effort with @tkadava.bsky.social @tshamorkina.bsky.social and @hecklab.bsky.social
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Reposted by Tatiana Shamorkina
Kermit Murray @kkmurray.bsky.social · 29/05/2025
(BioRxiv All) Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry: The ability to sequence proteins without reliance on a genomic template defines a critical frontier in modern proteomics.… #BioRxiv #MassSpecRSS
dlvr.it
Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry
The ability to sequence proteins without reliance on a genomic template defines a critical frontier in modern proteomics. This approach, known as de novo protein sequencing, is essential for applications such as antibody sequencing, microbiome proteomics, and antigen discovery, which require accurate reconstruction of peptide and protein sequences. While trypsin remains the gold-standard protease in proteomics, its restricted cleavage specificity limits peptide diversity. This constraint is especially problematic in antibody sequencing, where the functionally critical regions often lack canonical tryptic sites. As a result, exclusively trypsin-based approaches yield sparse reads, leading to sequence gaps. Multi-protease and hybrid-fragmentation strategies can improve the sequence coverage, but they add complexity, compromise scalability and reproducibility. Here, we explore two HyperThermoacidic Archaeal (HTA)-proteases as single-enzyme solutions for de novo antibody sequencing. Each HTA-protease generated about five times more unique peptide reads than trypsin or chymotrypsin, providing high redundancy across all CDRs. Combined with EAciD fragmentation on a ZenoTOF 7600 system, this approach enabled complete, unambiguous antibody sequencing. De novo analysis using PEAKS/DeepNovo and Stitch showed up to fourfold higher alignment scores and reduced the sequence errors within the HTA-generated data. Additionally, the HTA-EAciD approach offers short digestion times, eliminates extensive cleanup, and enables analysis in a single LC-MS/MS run. This streamlined, single-protease approach delivers therefore performance comparable to multi-enzyme workflows, offering a scalable and efficient strategy for de novo protein sequencing across diverse applications.
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Reposted by Tatiana Shamorkina
Tereza Kadavá @tkadava.bsky.social · 29/05/2025
Check out our new preprint on combining archeal proteases with hybrid fragmentation to streamline de novo antibody sequencing! Joined effort with @lperezpaneda.bsky.social, @tshamorkina.bsky.social, and @hecklab.bsky.social
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Reposted by Tatiana Shamorkina
Joost Snijder @joostsnijder.bsky.social · 23/05/2025
First time working on dolphin/whale viruses 🐬🦠🐳. Check out our new preprint with @danielhurdiss.bsky.social et al. describing the structure and glycan shield of two cetacean coronavirus spikes. Some neat glycoproteomics work by @tshamorkina.bsky.social in this one. www.biorxiv.org/content/10.1...
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Stephan Hacker @stephanhacker2.bsky.social · 17/01/2025
Very interesting talk by Tatiana Shamorkina from the @hecklab.bsky.social at #NPP2025. She talked about the challenge of sequencing antibodies using mass spectrometry. Cool insights into the application of the ZenoTOF and different fragmentation methods for long-read peptide sequencing.
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