PXD060367

PXD060367 is an original dataset announced via ProteomeXchange.

Title	Comparative analysis of three extraction method for simultaneous metabolomic and proteomic profiling
Description	The simultaneous analysis of the proteome and metabolome in biological samples is essential for advancing systems biology, enabling a deeper understanding of molecular mechanisms governing diverse biological processes. This study compares three extraction methods: the Bligh and Dyer method, the Matyash method, and a simple methanol extraction technique. This study was conduct on lyophilized potato tuber powder, a complex matrix containing starches, proteins, and a variety of metabolites. With the use of high-resolution mass spectrometry (HRMS), specifically nanoLC-MS/MS and direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FT-ICR-MS), we aimed to select one of these extraction methods to understand the behaviours of several potato cultivar facing cold stress. Our findings indicate that the Matyash and methanol extraction methods provided superior performance and reproducibility for proteomic analysis, while all methods offered similar results in metabolomic profiling. Moreover, the dual-phase extraction from the Bligh and Dyer and Matyash methods revealed distinct and complementary datasets, emphasizing the importance of multi-phase approaches for comprehensive molecular characterization. Despite some redundancy observed between polar and apolar phases, the overall analysis highlights the necessity of optimal extraction techniques for future proteomic and metabolomic studies. These results enhance our understanding of the potato tuber’s biological landscape.
HostingRepository	PRIDE
AnnounceDate	2026-02-09
AnnouncementXML	Submission_2026-02-09_00:57:37.447.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	BRAY FABRICE
SpeciesList	scientific name: Solanum tuberosum (Potato); NCBI TaxID: NEWT:4113;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Bruker Daltonics solarix series; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-30 07:17:28	ID requested
⏵ 1	2026-02-09 00:57:37	announced

10.1021/ACSAGSCITECH.5C00771;

submitter keyword: High resolution mass spectrometry, Metabolomics, Proteomics, Potato tubers, Starch,Multi-omics, Extraction methods

fabrice bray
contact affiliation	MSAP UAR 3290 CNRS avenue paul langevins 59655 villeneuve d'ascq france
contact email	fabrice.bray@univ-lille.fr
lab head
BRAY FABRICE
contact affiliation	MSAP USR 3290
contact email	fabrice.bray@univ-lille.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060367
     1. Label: PRIDE project
     2. Name: Comparative analysis of three extraction method for simultaneous metabolomic and proteomic profiling