Scientist focused in proteomics and mass spectrometry | Director of Proteomics R&D Broad Institute of MIT and Harvard | Mom | Fan of cheese
Joined May 2009
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Namrata Udeshi retweeted
Survey of mitochondria proteomes across eukaryotes explores organelle’s role, suggests mitochondria originated late in eukaryotic evolution, and highlights possible drug targets for tropical diseases. broad.io/MitoCartaTreeOfLife
Check out new work published in @ScienceMagazine from a wonderful collaboration led by the lab of @JiefuBiol @hhmi_science to map the luminal surface of brain vasculature proteome to uncover BBB regulators @BroadProteomics @broadinstitute
Luminal surface proteome of the brain vasculature uncovers blood-brain barrier regulators @ScienceMagazine:
science.org/doi/10.1126/scie…
Big thanks to Zijian, Zuzhi, Yupu, Khanh, Yuxiang, and all collaborators to make this possible!
Thrilled to see our study out in Nature Medicine led by @RemailehAbu and the Kaelin lab, revealing how HIF2-driven secreted proteins cause cachexia in kidney cancer. @broadinstitute @DanaFarber
Our paper is now officially published in @NatureMedicine!
Thrilled to share the final version online: nature.com/articles/s41591-0…
Thankful to my co-authors, collaborators, and our lab for the support.
@kaelin_lab @DrChoueiri @PitarresiLab @namude @DanaFarber
Namrata Udeshi retweeted
We are hiring a new lab manager! Our wonderful lab manager Albert is headed off to grad school and we are looking to fill his position this summer. This is a great opportunity for a new graduate to spend a couple years immersed in research before applying to PhD or MD programs. 50% of the job is keeping the lab running (being a lab manager), and 50% is for original research related to protein engineering, technology development, etc – there are many project possibilities!
Seeking passionate, motivated, creative, and detail-oriented majors in chemical biology, molecular biology or related subjects with at least 1 year of prior wetlab research experience. Must be a US citizen or have a valid work visa.
To apply: careersearch.stanford.edu/jo…
Check out our new work led by @aliceyting and her lab presenting LaccID for peroxide-free labeling of cell surface proteins for PL-proteomics and EM applications.
APEX peroxidase is a versatile tool for proximity labeling and electron microscopy (EM) but its requirement for toxic H2O2 is a liability. We now report LaccID, a multicopper oxidase evolved from an ancestral fungal laccase that oxidizes aromatic substrates using non-toxic O2 instead of H2O2. We use LaccID for EM imaging of cultured cells and fly brains, and for proteomic mapping of the changing surface composition of T cells that engage with tumor cells via antigen-specific T cell receptors.
Excited to share our latest manuscript dedicated to the remarkable Donald F. Hunt, a true pioneer in the field of mass spectrometry and O-GlcNAc research! From Fringe to the Mainstream: How ETD MS brought O-GlcNAc to the masses mcponline.org/article/S1535-…
A special thanks to my co-authors Chad Slawson and Gerald Hart for helping with this special tribute to Don and for their critical collaborations in the early 2000’s that shaped my Ph.D.
Grateful for the opportunity to learn from Don and Jeff @UVA, whose enthusiasm, curiosity and kindness have profoundly impacted my career.
#teamMassSpec #OGlcNAc #ETD #proteomics
Another terrific collaboration with @JiefuBiol lab and collaborators profiling cell surface proteome human dendritic cells.
Glad to share our latest study on the cell-surface proteome of human dendritic cells, by our awesome long-term collaborators Namrata and Charles @BroadProteomics and talented undergrad @Zuzhi_Jiang (soon at @UCSF tetrad for PhD).
journals.aai.org/jimmunol/ar…
Namrata Udeshi retweeted
Glad to share our latest study on the cell-surface proteome of human dendritic cells, by our awesome long-term collaborators Namrata and Charles @BroadProteomics and talented undergrad @Zuzhi_Jiang (soon at @UCSF tetrad for PhD).
journals.aai.org/jimmunol/ar…
If you’re at ASMS, check out these fantastic talks and posters from @BroadProteomics!! Talks will cover immunopeptidomics, proteogenomics of ODG and single-cell proteomics. Posters include our latest work in HDX-MS, TargetID, Olink vs. DIA-MS for plasma, and FFPE proteomics.
Please check out new work from @aliceyting and all co-authors using PL methods to study protein trafficking. Another fun and exciting collaboration with Alice and the entire team. @BroadProteomics
TransitID is out today in Cell! This is a proximity labeling method for unbiased discovery of endogenous proteins that traffick from a defined “source” location to a defined “destination” location. TransitID uses sequential labeling by TurboID in the source, followed by a chase period (minutes to hours) and then 1-minute APEX tagging in the destination compartment. Proteins tagged by both enzymes are enriched with streptavidin and anti-fluorescein antibody, and identified by mass spec.
We explore 4 intracellular and intercellular applications of TransitID:
- discovery of locally translated mitochondrial proteins (translated at OMM, then imported into mito matrix)
- mapping proteins whose cytoplasm-to-nucleus shuttling is dampened by stress
- discovery of proteins that transit between nucleolus & stress granules during stress & stress recovery
- analysis of proteins that traffic intercellularly bw tumor cells & macrophages
Work of amazingly talented co-first authors @WeiQinChemBio and @CheahJoleen, and collaborators Steve Carr @namude & Paul Taylor
authors.elsevier.com/a/1hKLc…
Namrata Udeshi retweeted
TransitID is out today in Cell! This is a proximity labeling method for unbiased discovery of endogenous proteins that traffick from a defined “source” location to a defined “destination” location. TransitID uses sequential labeling by TurboID in the source, followed by a chase period (minutes to hours) and then 1-minute APEX tagging in the destination compartment. Proteins tagged by both enzymes are enriched with streptavidin and anti-fluorescein antibody, and identified by mass spec.
We explore 4 intracellular and intercellular applications of TransitID:
- discovery of locally translated mitochondrial proteins (translated at OMM, then imported into mito matrix)
- mapping proteins whose cytoplasm-to-nucleus shuttling is dampened by stress
- discovery of proteins that transit between nucleolus & stress granules during stress & stress recovery
- analysis of proteins that traffic intercellularly bw tumor cells & macrophages
Work of amazingly talented co-first authors @WeiQinChemBio and @CheahJoleen, and collaborators Steve Carr @namude & Paul Taylor
authors.elsevier.com/a/1hKLc…
We hope you check out the great work presented by these outstanding scientists @BroadProteomics during #ASMS2023.
If you’re at #ASMS2033 this week come check out these talks and posters by members of the Broad Proteomics Team!!
Namrata Udeshi retweeted
LOV-Turbo is published today in @naturemethods and plasmids for LOV-Turbo are available on Addgene, here:
addgene.org/browse/article/2…
We hope many people will use LOV-Turbo in exciting new ways!
nature.com/articles/s41592-0…
If you plan to use NanoLuc BRET to activate LOV-Turbo, please reach out, as we are engineering improved LOV-Turbo + NanoLuc variants with higher BRET efficiency.
Light-regulated TurboID, or LOV-Turbo, is a feat of engineered allostery, created by @SongyiLee10 and @CheahJoleen via structure-guided design, then optimized by yeast display directed evolution. Activity is nearly undetectable in the dark state, but increases within seconds to a level comparable to TurboID after weak blue-light illumination. Removing light shuts LOV-Turbo off again (ie, it is reversible).
LOV-Turbo is easy to use in mammalian cells, yeast, bacteria, and even in the mouse brain to suppress background labeling from endogenous biotin, to perform pulse-chase proteomics, and to spatially control biotinylation.
We also show that instead of external blue light, LOV-Turbo can be activated by genetically-encoded light, ie bioluminescence from luciferase, via BRET (Figure 4F-I).
Huge thanks to incredibly talented co-first authors @SongyiLee10 and @CheahJoleen, and our wonderful collaborators Steve Carr and @namude. Also many thanks to co-authors @Simenzhao, Charles Wu, @heegwangroh, @tinakim_neuro and @kelvinfcho for their contributions.
Plasmids will be available on Addgene in the near future!
biorxiv.org/cgi/content/shor…
