Sep 01, 2022

Public workspaceOverall protocol for MicroPOTS LCMS top down proteomics of kidney tissue sections

DOI
https://dx.doi.org/10.17504/protocols.io.eq2lynm1qvx9/v1
  • Mowei Zhou1,
  • James M Fulcher1,
  • Yen-Chen Liao1,
  • Ljiljana.PasaTolic 1
  • 1Pacific Northwest National Laboratory
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
  • PNNL-TTD
Mowei Zhou
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DOI: https://dx.doi.org/10.17504/protocols.io.eq2lynm1qvx9/v1
Protocol Citation: Mowei Zhou, James M Fulcher, Yen-Chen Liao, Ljiljana.PasaTolic 2022. Overall protocol for MicroPOTS LCMS top down proteomics of kidney tissue sections. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2lynm1qvx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 18, 2022
Last Modified: September 01, 2022
Protocol Integer ID: 68871
Keywords: proteomics of kidney tissue section, proteomics of kidney, micropots lcm, proteomic, overall protocol for micropots lcm, kidney tissue section, micropots platform, proteoform identification, overall workflow for lcm, lcm, tissue functional unit, kidney, functional units from tissue section, selected tissue
Funders Acknowledgements:
National Institutes of Health (NIH) Common Fund, Human Biomolecular Atlas Program (HuBMAP)
Grant ID: UG3CA256959-01
Abstract
This is the overall workflow for LCMS top down proteomics of kidney functional units from tissue sections using the MicroPOTS platform. The expected outcomes are proteoform identification and quantitation values from selected tissue functional units.
Troubleshooting
Tissue collection
The tissue sections were prepared and shipped from Vanderbilt-TMC following the protocol below:

Protocol
NAME

Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging

CREATED BY
Jamie Allen

Sample preparation
Functional units (glomerulus, medullary, tubule) were dissected and collected into the microPOTS platform using the method below:
Protocol
NAME
Laser Capture Microdissection of Tissue Functional Units for microPOTS Top-Down Proteomics
CREATED BY
James M Fulcher

Data Acquisition
The samples were analyzed by LCMS top down proteomics as described below:
Protocol
NAME
Top Down Proteomics Data Collection for Microdissected Kidney Tissue Functional Units
CREATED BY
Mowei Zhou

Data Analysis
LCMS datasets were analyzed for proteoform identification and quantitation. The final results are reported.
Protocol
NAME
Proteoform Identification and Quantitation with TopPIC and TDPortal for Human Tissues
CREATED BY
Mowei Zhou