PXD003150

PXD003150 is an original dataset announced via ProteomeXchange.

Title	Protein stable isotope fingerprinting (P-SIF): Synechocystis sp. PCC6803 + Allochromatium vinosum DSM180 biomass mixture
Description	Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determining the values of δ13C for different taxonomic divisions, and (ii) using those values as clues to the metabolic pathways employed by the respective organisms. This project develops a two-dimensional HPLC protocol followed by tryptic digestion and isotope ratio mass spectrometry on fraction aliquots. Data from a mixture of Synechocystis sp. PCC6803 and A. vinosum DSM180 biomass show that P-SIF can predict the δ13C values of the original taxa. The measured values of δ13C along with the QTOF-MS/MS peptide signal intensity and protein assignments are used in an overdetermined set of linear equations to back-calculate the values of δAllo and δSyn for the individual species. These data suggest the approach will be useful to determine natural δ13C signatures in microbial ecosystems.
HostingRepository	PRIDE
AnnounceDate	2015-11-10
AnnouncementXML	Submission_2015-11-10_04:10:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Susan Carter
SpeciesList	scientific name: Synechocystis sp. PCC 6803; NCBI TaxID: 1148; scientific name: Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (Chromatium vinosum); NCBI TaxID: 572477;
ModificationList	No PTMs are included in the dataset
Instrument	6520 Quadrupole Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2015-11-05 02:29:16	ID requested
⏵ 1	2015-11-10 04:10:03	announced

Dataset with its publication pending

curator keyword: Metaproteomics, Biological

submitter keyword: Culture studies, chemostats, photosynthetic species, LC-QToF-MS/MS

Ann Pearson
contact affiliation	Murray and Martha Ross Professor of Environmental Sciences, Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA USA
contact email	apearson@eps.harvard.edu
lab head
Susan Carter
contact affiliation	Harvard University
contact email	sjcarter@fas.harvard.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/2015/11/PXD003150

PRIDE project URI

• PRIDE
  1. PXD003150
     1. Label: PRIDE project
     2. Name: Protein stable isotope fingerprinting (P-SIF): Synechocystis sp. PCC6803 + Allochromatium vinosum DSM180 biomass mixture