Saketh Kapoor, PhD
@Sakethkapoor
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Associate Research Scientist & Lab Manager @yalemed | Spatial Proteomics Specialist | Cancer Proteomics | Single Cell Proteomics | Clearomics | timsTOF
New Haven, CT
Joined February 2010
🚨New preprint alert!! Introducing "GlycoFASP" - a super easy method to isolate pure O-glycopeptides from complex samples. Pioneered by Shane and @keira_erol, they show that you can simply add sample + glycoprotease to a MWCO filter -> O-glycopeptides 10.26434/chemrxiv-2025-bxv0k
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Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!
High-dimensional imaging using combinatorial channel multiplexing and deep learning https://t.co/balOMNQew0
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As a scientist, David is laser-focused on developing protein design as a platform. The moment a design goal becomes well-established, he pushes the lab to move on to new modalities. For example, for a long time, the goal was to make proteins that could bind to other proteins. But
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Now online - check out this video from @StrubeStiftung where @JulianeWalz introduces our new phase I #ClinicalTrial for an #immunopeptidomics-based #peptide #vaccine for #patients with #AML. https://t.co/dkHnMz6dew
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A protocol paper describing how to acquire and analyze multiplex DIA (mDIA) special proteomics data, with a tutorial on building a spectral library from ddaPASEF using #FragPipe. And now with diaTracer in FragPipe22, you can build a hybrid DDA+DIA library!
link.springer.com
Spatially resolved mass spectrometry-based proteomics at single-cell resolution promises to provide insights into biological heterogeneity. We describe a protocol based on multiplexed data-independ...
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Two papers in @Nature present a new genome editing technique that enables the insertion, inversion and deletion of long DNA sequences at user-specified genome positions. The approach may provide an easier method of genome editing. https://t.co/EwMQtgoTrE
https://t.co/ecUGLy4l2O
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So excited to host Prof. Lingjun Li @LiResearch from @UWMadison, an esteemed leader in mass spectrometry, at @YalePharm!! Join us tomorrow, June 27th, at 12:30 PM in Brady Auditorium for her talk on "Advancing Biomedical Research via Innovation in MS-based Approaches." @YaleMed
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Friends, #FragPipe 22 has been released, and it's a big update! diaTracer enables spectrum-centric analysis of diaPASEF data. Skyline integration. Koina server for more deep-learning prediction options. DDA+ mode for ddaPASEF. DIA glycoproteomics and new chemoproteomics workflows
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Absolutely thrilled to see our paper on a VR-trained deep learning pipeline for mapping mouse brain cells published in @NatureMethods 🤩 Retrainable via Fiji for custom data, we used it to study brain activities in cancer.
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Very nice birthday present for Albert. The first timsOmni trap is currently being delivered to Albert’s lab.
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New mass spectrometry techniques significantly enhance the detection of HLA class I peptide ligands, paving the way for targeted vaccine and #immunotherapy development ⚡️ #immunopeptidome
nature.com
Nature Communications - Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are targets for developing vaccines and immunotherapies. Here the authors report Thunder-DDA-PASEF, an...
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T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery
biorxiv.org
Effective, unbiased, high-throughput methods to functionally identify both class II and class I HLA-presented T cell epitopes and their cognate T cell receptors (TCRs) are essential for and prerequ...
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The championship round is here.. Vote #TeamMassSpec.. Let's show CRISPR how the champions do.. https://t.co/QhzvDt65ZN
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Happy to contribute to this study. Group-specific FDR estimation is one of the strategies to control the error rates in proteogenomics searches for noncanonical peptides. There is tutorial on how to annotate the database and perform group FDR in #FragPipe:
fragpipe.nesvilab.org
A complete proteomics pipeline with the MSFragger search engine at heart
Our new study, spearheaded by Humberto Ferreira, is available online. We delve into the detection of HLA peptides that may originate from the translation of circRNAs. Special thanks to the @nesvilab for setting up the group-specific FDR control in FragPipe
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Want to learn how to optimize your #DDA-PASEF acquisition for #immunopeptidomics? Use Thunder-DDA-PASEF! See our paper by @DavidGomezZep from @HITRONMainz: https://t.co/ioN3CJVqII Thanks to a wonderful collaboration with @compomics and @ChristineCARAP1!
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#TeamMassSpec We're recruiting postdocs to work on new methods to map proteome remodeling due to chemical perturbations, aging, development, and more! If you're interested, see the job posting: https://t.co/Lr62QwEVrM and some of the lab's projects:
schweppelab.org
Chemoproteomics
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Yet another must read from @NanoPOTS_SCP (nice to see @fcyucn and @nesvilab on there too!). Impressive depth and throughput for 50µm spatial resolution. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows
biorxiv.org
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in both normal and diseased tissues. Proteome-sc...
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A dream of our lab has been to image the full central dogma from a single endogenous gene, all live and with single molecule resolution. After many years we are happy to unveil a beautiful cell line that makes it possible. Check out our preprint ( https://t.co/Fb7L1fYFRn)! (1/n)
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Do you need an intro to analyzing (prote)omics data? This series of lectures may be helpful. We aimed to make them short & accessible. Enjoy watching & learning! https://t.co/OOFPs3dhXK
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