Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets

Zhu, Ying; Dou, Maowei; Piehowski, Paul D.; Liang, Yiran; Wang, Fangjun; Chu, Rosalie K.; Chrisler, William B.; Smith, Jordan N.; Schwarz, Kaitlynn C.; Shen, Yufeng; Shukla, Anil K.; Moore, Ronald J.; Smith, Richard D.; Qian, Wei-Jun; Kelly, Ryan T.

doi:10.1074/mcp.TIR118.000686

Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets

Journal Article · Sun Jun 24 04:00:00 EDT 2018 · Molecular and Cellular Proteomics

DOI:https://doi.org/10.1074/mcp.TIR118.000686· OSTI ID:1503624

; Dou, Maowei; ; Liang, Yiran; ; Chu, Rosalie K.; Chrisler, William B.; Smith, Jordan N.; Schwarz, Kaitlynn C.; Shen, Yufeng; Shukla, Anil K.; Moore, Ronald J.; ; ;

Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution because of the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 µm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-µm-thick rat brain cortex tissue sections having diameters of 50, 100, and 200 µm, respectively. We also analyzed 100-µm-diameter sections corresponding to 10–18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1503624

Report Number(s):: PNNL-SA-138815

Journal Information:: Molecular and Cellular Proteomics, Journal Name: Molecular and Cellular Proteomics Journal Issue: 9 Vol. 17; ISSN 1535-9476

Publisher:: American Society for Biochemistry and Molecular Biology

Country of Publication:: United States

Language:: English

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