PXD041958

PXD041958 is an original dataset announced via ProteomeXchange.

Title	Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-07-02
AnnouncementXML	Submission_2024-07-02_06:03:23.017.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yi Xiong
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-03 16:45:59	ID requested
1	2024-06-14 07:43:01	announced
⏵ 2	2024-07-02 06:03:23	announced	2024-07-02: Updated project metadata.

10.1074/mcp.m110.006049;

Pan C, Fischer CR, Hyatt D, Bowen BP, Hettich RL, Banfield JF, Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteomics, 10(4):M110.006049(2011) [pubmed]

submitter keyword: proteomics, 15N labeling, stable isotope,SIP

Chongle Pan
contact affiliation	The Department of Microbiology and Plant Biology,the University of Oklahoma
contact email	cpan@ou.edu
lab head
Yi Xiong
contact affiliation	The School of Biological Sciences, The University of Oklahoma
contact email	yixiong@ou.edu
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/2024/06/PXD041958

PRIDE project URI

• PRIDE
  1. PXD041958
     1. Label: PRIDE project
     2. Name: Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities