PXD060073-1

PXD060073 is an original dataset announced via ProteomeXchange.

Title	MALDI-MSI-guided LCM-MS: Advancing spatial multi-omics in mouse brain tissue
Description	Spatial multi-omics involves the analysis of biomolecules such as proteome, metabolome, and lipidome within their native spatial context in tissues or cells. This approach provides a comprehensive understanding of biomolecular networks in specific biological environments. Mass spectrometry imaging (MSI) has emerged as a powerful technique for mapping the region-specific molecular distribution in regions of interest (ROIs) with its high spatial resolution. Laser capture microdissection-based mass spectrometry (LCM-MS) is another well-established workflow for spatial multi-omics, allowing the reliable characterization of biomolecules in ROIs with the high sensitivity. To advance the current analytical application, we introduce matrix-assisted laser desorption/ionization (MALDI)-MSI-guided LCM-MS approach that integrates MALDI-MSI metabolomics with LCM sample-based LC-MS/MS metabolomics and proteomics. As a proof of concept, we applied this approach to mouse brain tissue. MALDI-MSI identified over 300 putative metabolites and lipids, with high abundance of PE (36:0), PC (38:4), and PG (38:4) in the hippocampus and PI (36:4), PE (38:6), and docosahexaenoic acid in the cortex regions, respectively. Both hippocampus and cortex regions were isolated as two ROIs using LCM, followed by LC-MS/MS-based metabolomics, lipidomics and proteomics. LCM-metabolomics annotated 186 compounds encompassing small molecules and lipids. Several molecules revealed the distinct molecular abundance between the two regions. Importantly, acetylcholine (ACh), acetyl-L-carnitine (ALCAR), inosine, and nicotinamide exhibited noticeable up-regulation in the hippocampus, consistent with previous reports. LCM-proteomics identified over 3,500 proteins across the two ROI regions, with 796 differentially expressed proteins (DEPs). Of these, 498 and 298 proteins showed significantly more abundant in the cortex and hippocampus regions, respectively. Biological network analysis using DEPs highlighted that their molecular pathway and phenotype showed strongly aligned with region-specific characteristic. Our MALDI-MSI-guided LCM-MS approach enables comprehensive profiling and quantitative analysis of proteome, metabolome, and lipidome, providing valuable insights into complex biological systems and spatial molecular distribution.
HostingRepository	PRIDE
AnnounceDate	2026-09-07
AnnouncementXML	Submission_2026-09-06_16:25:23.875.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD060073
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Byoung-Kyu Cho
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-22 12:46:46	ID requested
⏵ 1	2026-09-06 16:25:24	announced

10.3390/life16071177;

Cho BK, Lukowski JK, Son M, Zamacona Calderon A, Levi M, Stumpo K, Snyder S, Esterling M, Goo YA, MALDI-MSI-Guided Laser Capture Microdissection Coupled with MS for Integrated Spatial Multi-Omics in Mouse Brain. Life (Basel), 16(7):(2026) [pubmed]

10.6019/PXD060073;

submitter keyword: LCM-MS,Spatial omics, MALDI-MSI

Young Ah Goo
contact affiliation	Washington University in St. Louis
contact email	ygoo@wustl.edu
lab head
Byoung-Kyu Cho
contact affiliation	Washington University in St. Louis
contact email	byoung-kyu@wustl.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060073
     1. Label: PRIDE project
     2. Name: MALDI-MSI-guided LCM-MS: Advancing spatial multi-omics in mouse brain tissue