Proteomics

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Spatially resolved top-down proteomics of tissue sections based on a microfluidic nanodroplet sample preparation platform

ABSTRACT: We demonstrate spatially resolved top-down proteomics (TDP) for proteoform identification and quantification from small sections of rat brain. We used the nanoPOTS (nanodroplet Processing in One pot for Trace Samples) platform, further improving the sample preparation by adding benzonase in the extraction buffer. We increased identified proteoforms from 493 to 700 in 200 cultured cells, with the largest improvements among nuclear proteins. We then performed nanoPOTS TDP on 100,000 um2 (around 200 cells) laser capture microdissectioned rat brain cortex/hypothalamus tissues. The extracted proteins were directly subjected to top down analysis without enzymatic digestion. Data was searched with TopPIC and TDPortal.

INSTRUMENT(S): Orbitrap Eclipse, Orbitrap Fusion Lumos

ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116) Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Mowei Zhou  

PROVIDER: MSV000089163 | MassIVE | Wed Mar 30 09:24:00 BST 2022

REPOSITORIES: MassIVE

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Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform.

Liao Yen-Chen YC   Fulcher James M JM   Degnan David J DJ   Williams Sarah M SM   Bramer Lisa M LM   Veličković Dušan D   Zemaitis Kevin J KJ   Veličković Marija M   Sontag Ryan L RL   Moore Ronald J RJ   Paša-Tolić Ljiljana L   Zhu Ying Y   Zhou Mowei M  

Molecular & cellular proteomics : MCP 20230102 2

Conventional proteomic approaches measure the averaged signal from mixed cell populations or bulk tissues, leading to the dilution of signals arising from subpopulations of cells that might serve as important biomarkers. Recent developments in bottom-up proteomics have enabled spatial mapping of cellular heterogeneity in tissue microenvironments. However, bottom-up proteomics cannot unambiguously define and quantify proteoforms, which are intact (i.e., functional) forms of proteins capturing gen  ...[more]

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