Dataset Information

Optimizing MS-based multi-omics: comparative analysis of protein, metabolite, and lipid extraction techniques

ABSTRACT: Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, complexity of data pre-processing, and reproducibility concerns. Although conventional pre-processing methods in multi-omics research are standardized to ensure consistency; their simultaneous application can obscure specific details. Here, findings obtained from various omics approaches were profiled using various extraction methods (methanol extraction, Folch method, and Matyash methods for metabolites and lipids) and two digestion methods (Filter-aided sample preparation (FASP) and suspension traps (S-Trap)) for resuspended proteins. FASP was found to be more effective for separation of membrane-related proteins, whereas S-Trap excelled in isolating nuclear-related and RNA processing proteins. Thus, ASP may be suitable for investigating the immune response and bacterial infection pathways, whereas S-Trap may be more effective for studies focused on the mechanisms of neurodegenerative diseases. Moreover, the choice of extraction method, either single-phase MeOH or two-phase using Folch and Matyash methods, significantly influences the types of compounds identified, reflecting distinct profiles in different omics data sets. Among metabolites, the single-phase methd identified organic compounds and compounds related to fatty acids, whereas the two-phase extraction identified more hydrophilic compounds such as nucleotides. Lipids with strong hydrophobicity, such as ChE and TG, were identified in the two-phase extraction results. These findings highlight that significant differences between small molecules identified are primarily due to varying polarities of extraction solvents. To address human error and batch effects, a strategy that optimizes the balance between efficiency and the quality of the results is also proposed here. Our study reaffirms the impact of choice of pre-processing method in multi-omics, and also provides specific profiles of several protein and metabolite clusters as well as lipid classes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver, Epithelial Cell

SUBMITTER: Jeong-hun Mok

LAB HEAD: Hookeun Lee

PROVIDER: PXD047010 | Pride | 2024-05-22

REPOSITORIES: Pride

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Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques.

Mok Jeong-Hun JH Joo Minjoong M Cho Seonghyeon S Duong Van-An VA Song Haneul H Park Jong-Moon JM Lee Hookeun H

Metabolites 20240103 1

Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, the complexity of data pre-processing, and reproducibility concerns. Furthermore, existing studies have primarily focused on technical performance assessment and the presentation of modified protocols through ...[more]

PMID: 38248837

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			Action	DRS
	20201109_Multi-omics.pdStudy	Other
	20201109_Multi.msf	Msf
	20201109_Multi_P.msf	Msf
	20201109_Multi_P.pdResult	Other
	20201109_Multi_P1-1.raw	Raw