Tatiana Shamorkina

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

Thanks to @cinderbio.bsky.social and @sciex.bsky.social for their contribution and support

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

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

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.

(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

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

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...

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.