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De novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition

ABSTRACT: Dataset generated and used in "De novo assembled databases allow species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition". For more information, see SDRF.sdrf.tsv

INSTRUMENT(S):

ORGANISM(S): Bacteria Candidatus Kuenenia Stuttgartiensis

TISSUE(S): Cell Suspension Culture

SUBMITTER: Simon Klaes

LAB HEAD: Lorenz Adrian

PROVIDER: PXD057215 | Pride | 2025-09-08

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	01_6_27_12C_01.mztab	Mztab
	01_6_27_12C_01.raw	Raw
	01_6_27_12C_01.tsv	Tabular
	02_6_27_12C_02.mztab	Mztab
	02_6_27_12C_02.raw	Raw

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Publications

De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.

Klaes Simon S White Christian C Alvarez-Cohen Lisa L Adrian Lorenz L Ding Chang C

Environmental microbiome 20250826 1

BACKGROUND: Protein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbial communities. In Protein-SIP, peptides and corresponding taxa are identified by database matching, making database quality crucial for accurate analyses. For samples with unknown community composition, Protein-SIP typically employs either unrestricted reference ...[more]

PMID: 40859350

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