TY - JOUR
T1 - MALDI-MSI-LC-MS/MS Workflow for Single-Section Single Step Combined Proteomics and Quantitative Lipidomics
AU - Hendriks, Tim F.E.
AU - Krestensen, Kasper K.
AU - Mohren, Ronny
AU - Vandenbosch, Michiel
AU - De Vleeschouwer, Steven
AU - Heeren, Ron M.A.
AU - Cuypers, Eva
N1 - Funding Information:
This research has been made possible with the support of the NWO STEM (Project Number 19013 to E.C.), which is financed by The Netherlands Organization for Scientific Research. This research is part of the LINK program, which is financially supported by the Dutch Province of Limburg. We gratefully acknowledge the support of the FWO Research Foundation, Belgium (TBM T001919N). The authors are thankful to the Department of Neurosurgery of KU Leuven for providing the GBM sample, R. Sciot for annotating the H&E staining, S. Tortorella and G. Sorbi for implementing the LMD-code in LipostarMSI v2.0. Figures were created via BioRender.com .
Publisher Copyright:
© 2024 The Authors. Published by American Chemical Society.
PY - 2024/3/4
Y1 - 2024/3/4
N2 - We introduce a novel approach for comprehensive molecular profiling in biological samples. Our single-section methodology combines quantitative mass spectrometry imaging (Q-MSI) and a single step extraction protocol enabling lipidomic and proteomic liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis on the same tissue area. The integration of spatially correlated lipidomic and proteomic data on a single tissue section allows for a comprehensive interpretation of the molecular landscape. Comparing Q-MSI and Q-LC-MS/MS quantification results sheds new light on the effect of MSI and related sample preparation. Performing MSI before Q-LC-MS on the same tissue section led to fewer protein identifications and a lower correlation between lipid quantification results. Also, the critical role and influence of internal standards in Q-MSI for accurate quantification is highlighted. Testing various slide types and the evaluation of different workflows for single-section spatial multiomics analysis emphasized the need for critical evaluation of Q-MSI data. These findings highlight the necessity for robust quantification methods comparable to current gold-standard LC-MS/MS techniques. The spatial information from MSI allowed region-specific insights within heterogeneous tissues, as demonstrated for glioblastoma multiforme. Additionally, our workflow demonstrated the efficiency of a single step extraction for lipidomic and proteomic analyses on the same tissue area, enabling the examination of significantly altered proteins and lipids within distinct regions of a single section. The integration of these insights into a lipid-protein interaction network expands the biological information attainable from a tissue section, highlighting the potential of this comprehensive approach for advancing spatial multiomics research.
AB - We introduce a novel approach for comprehensive molecular profiling in biological samples. Our single-section methodology combines quantitative mass spectrometry imaging (Q-MSI) and a single step extraction protocol enabling lipidomic and proteomic liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis on the same tissue area. The integration of spatially correlated lipidomic and proteomic data on a single tissue section allows for a comprehensive interpretation of the molecular landscape. Comparing Q-MSI and Q-LC-MS/MS quantification results sheds new light on the effect of MSI and related sample preparation. Performing MSI before Q-LC-MS on the same tissue section led to fewer protein identifications and a lower correlation between lipid quantification results. Also, the critical role and influence of internal standards in Q-MSI for accurate quantification is highlighted. Testing various slide types and the evaluation of different workflows for single-section spatial multiomics analysis emphasized the need for critical evaluation of Q-MSI data. These findings highlight the necessity for robust quantification methods comparable to current gold-standard LC-MS/MS techniques. The spatial information from MSI allowed region-specific insights within heterogeneous tissues, as demonstrated for glioblastoma multiforme. Additionally, our workflow demonstrated the efficiency of a single step extraction for lipidomic and proteomic analyses on the same tissue area, enabling the examination of significantly altered proteins and lipids within distinct regions of a single section. The integration of these insights into a lipid-protein interaction network expands the biological information attainable from a tissue section, highlighting the potential of this comprehensive approach for advancing spatial multiomics research.
U2 - 10.1021/acs.analchem.3c05850
DO - 10.1021/acs.analchem.3c05850
M3 - Article
SN - 0003-2700
VL - 96
SP - 4266
EP - 4274
JO - Analytical Chemistry
JF - Analytical Chemistry
IS - 10
ER -