MassIVE MSV000093925

Complete Public PXD048911

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

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Description

Existing spatially-resolved proteomics technologies cannot provide deep proteome coverage 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), multiplexed isobaric labelling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram level of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5,000 unique proteins from a small-sized human pancreatic tissue pixel (~60,000 um2) and differentiate unique protein abundance patterns in pancreas. Further, the use of microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories. [doi:10.25345/C5ZG6GJ5P] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: spatial proteomics ; pancreas ; islet

Contact

Principal Investigators:
(in alphabetical order) 		Paul D. Piehowski, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Veli?kovi? M, Fillmore TL, Attah IK, Posso C, Pino JC, Zhao R, Williams SM, Veli?kovi? D, Jacobs JM, Burnum-Johnson KE, Zhu Y, Piehowski PD.
Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment.
Anal Chem. 2024 Aug 13;96(32):12973-12982. Epub 2024 Aug 1.

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