PXD047010-1

PXD047010 is an original dataset announced via ProteomeXchange.

Title	Optimizing MS-based multi-omics: comparative analysis of protein, metabolite, and lipid extraction techniques
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-05-22
AnnouncementXML	Submission_2024-05-22_02:23:26.895.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeonghun Mok
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-16 01:42:11	ID requested
⏵ 1	2024-05-22 02:23:27	announced
2	2024-10-22 06:41:11	announced	2024-10-22: Updated project metadata.

Mok JH, Joo M, Cho S, Duong VA, Song H, Park JM, Lee H, Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques. Metabolites, 14(1):(2024) [pubmed]

10.3390/metabo14010034;

submitter keyword: LC-MS, FASP, Matyash method, S-trap,Multi-omics, Folch method

Hookeun Lee
contact affiliation	College of Pharmacy, Gachon University, 534-2 Yeonsu 3-dong, Yeonsu-gu, Incheon 406-799, Republic of Korea
contact email	hklee@gachon.ac.kr
lab head
Jeonghun Mok
contact affiliation	Department of Medical Device Management and Research, SAIHST, Sungkyunkwan University, Seoul 06355, Korea
contact email	jeonghunmok@naver.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/05/PXD047010

PRIDE project URI

• PRIDE
  1. PXD047010
     1. Label: PRIDE project
     2. Name: Optimizing MS-based multi-omics: comparative analysis of protein, metabolite, and lipid extraction techniques