Dataset Information

Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

ABSTRACT: Stable isotope probing (SIP) has been used to track nu- trient flows in microbial communities, but existing pro- tein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identi- fies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences be- tween closely related protein sequences, and for detect- ing labeling patterns in low-abundance proteins or pro- teins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, 50%, and 98%. The method was then used to monitor incorporation of 15 N into established and regrow- ing microbial biofilms. The results indicate organism-spe- cific migration patterns from established communities into regrowing communities and provide insights into me- tabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of 13 C or 15 N in microbial communities. Molecular and Cellular Proteomics 10: 10.1074/mcp.M110.006049, 1–11, 2011.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Escherichia Coli

SUBMITTER: Yi Xiong

LAB HEAD: Chongle Pan

PROVIDER: PXD041958 | Pride | 2024-06-14

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	0Percent.psm.txt	Txt
	50Percent.psm.txt	Txt
	98Percent.psm.txt	Txt
	AMD_DynamicSIP_SampleD_TimePoint0_BRmixed_WC_Velos_OrbiMS2_Run2_020210_02.raw	Raw
	AMD_DynamicSIP_SampleD_TimePoint0_BRmixed_WC_Velos_OrbiMS2_Run2_020210_03.raw	Raw

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Publications

Quantitative tracking of isotope flows in proteomes of microbial communities.

Pan Chongle C Fischer Curt R CR Hyatt Doug D Bowen Benjamin P BP Hettich Robert L RL Banfield Jillian F JF

Molecular & cellular proteomics : MCP 20110201 4

Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make ...[more]

PMID: 21285414

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