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Coupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment. | LitMetric

AI Article Synopsis

  • There is a growing interest in detailed proteomic methods to analyze tissue diversity at the level of individual cell types, which can enhance our understanding of complex biological systems like human organs.
  • Current spatially resolved proteomics techniques struggle with depth and sensitivity in profiling due to poor sample recovery.
  • The study successfully integrates laser capture microdissection with advanced microfluidic processing and peptide fractionation, enabling the identification of over 5,000 unique proteins from tiny pancreatic tissue samples, revealing distinct microenvironments within islets.

Article Abstract

There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity at a cell-type-specific level to better understand and predict the function of complex biological systems, such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverages due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (Microdroplet Processing in One pot for Trace Samples), the multiplexed isobaric labelling, and a nanoflow peptide fractionation approach. The integrated workflow allowed to maximize proteome coverage of laser-isolated tissue samples containing nanogram proteins. We demonstrated the deep spatial proteomics can quantify more than 5,000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 µm2) and reveal unique islet microenvironments.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055005PMC
http://dx.doi.org/10.1101/2023.03.13.531822DOI Listing

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