PXD042868-1

PXD042868 is an original dataset announced via ProteomeXchange.

Title	Integrative metabolomics and proteomics allow the global intracellular characterization of Bacillus subtilis cells and spores.
Description	Reliable and comprehensive multi-omics analysis is essential for researchers to understand and explore complex biological systems more completely. Bacillus subtilis is a model organism for Gram-positive spore-forming bacteria, and in-depth insight into the physiology and molecular basis of spore formation and germination in this organism requires advanced multilayer molecular datasets generated from the same sample. In this study, we evaluated two monophasic methods for polar and nonpolar compound extraction (acetonitrile/methanol/water; isopropanol/water, and 60% ethanol), and two biphasic methods (chloroform/methanol/water, and methyl tert-butyl ether/methanol/water) on coefficients of variation of analytes, identified metabolite composition and the quality of proteomics profiles. The analytical workflow comprises (1) parallel metabolite and protein extraction, (2) monophasic or biphasic sample extraction, (3) proteomics comparison and (4) multi-omics-based data visualization. The 60% EtOH protocol proved to be the easiest in sample processing and more amenable to automation. Collectively, we annotated 505 and 484 metabolites and identified 1665 and 1562 proteins in B. subtilis vegetative cells and spores, respectively. We also show differences between vegetative cells and spores from a multi-omics perspective and demonstrated that an integrative multi-omics analysis can be implemented from one sample using the 60% EtOH protocol. Correlation analysis further demonstrated that the metabolome and proteome datasets were highly correlated in content for components annotated to be part of the pyrimidine metabolism pathway. The results obtained by the 60% EtOH protocol provide a comprehensive insight into differences in the metabolic and protein makeup of B. subtilis vegetative cells and spores.
HostingRepository	MassIVE
AnnounceDate	2023-06-22
AnnouncementXML	Submission_2023-06-22_11:16:55.755.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gertjan Kramer
SpeciesList	scientific name: Bacillus subtilis; NCBI TaxID: 1423;
ModificationList	Oxidation; Carbamidomethyl
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-10 03:20:17	ID requested
⏵ 1	2023-06-22 11:16:56	announced

Yixuan Huang, Bhagyashree N. Swarge, Winfried Roseboom, Jurre D. Bleeker, Stanley Brul, Peter Setlow, Gertjan Kramer. Integrative metabolomics and proteomics allow the global intracellular characterization of Bacillus subtilis cells and spores. bioRxiv 2023.06.19.545067

doi: https://doi.org/10.1101/2023.06.19.545067 (preprint).

submitter keyword: Multi-omics, Metabolomics, Lipidomics, Proteomics, Gram positive, Bacteria, Spores, B. subtilis

Gertjan Kramer
contact affiliation	Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam
contact email	gertjan.kramer@uva.nl
lab head
Gertjan Kramer
contact affiliation	Universiteit van Amsterdam
contact email	gertjan.kramer@uva.nl
dataset submitter

MassIVE dataset URI

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