PXD006762

PXD006762 is an original dataset announced via ProteomeXchange.

Title	Proteomes of twenty bacterial, archaeal and eukaryotic species for bench marking of Direct Protein-SIF (stable carbon isotope fingerprinting proteomics)
Description	We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. To benchmark this method, we measured twenty pure culture species using the Direct Protein-SIF method as well as Isotope Ratio Mass Spectrometry. Some of the pure cultures were measured in technical replicates to see how consistent Protein-SIF measurements are between mass spec runs. This submission thus contains 29 raw files for the pure cultures. See table in the submission for details of which species was measured for which .raw file. We also included the Direct Protein-SIF specific isotope pattern files as well as the .mzML files and PSM files required as input for the Direct Protein-SIF software. In addition to the pure culture a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are also included in this submission (see publication for details on how the reference material is used to calibrate the method).
HostingRepository	PRIDE
AnnounceDate	2018-05-21
AnnouncementXML	Submission_2019-02-18_07:39:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Kleiner
SpeciesList	scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055; scientific name: Nitrososphaera viennensis; NCBI TaxID: 1034015; scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-21 01:24:37	ID requested
1	2018-05-21 02:48:44	announced
⏵ 2	2019-02-18 07:39:17	announced	Updated publication reference for PubMed record(s): 29844191.

Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, Strous M, Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A, 115(24):E5576-E5584(2018) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: LC-MS/MS, Metaproteomics, Protein-SIF, P-SIF, stable isotopes, stable carbon isotope fingerprinting

Marc Strous
contact affiliation	University of Calgary
contact email	mstrous@ucalgary.ca
lab head
Manuel Kleiner
contact affiliation	North Carolina State University
contact email	manuel_kleiner@ncsu.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/2018/05/PXD006762

PRIDE project URI

• PRIDE
  1. PXD006762
     1. Label: PRIDE project
     2. Name: Proteomes of twenty bacterial, archaeal and eukaryotic species for bench marking of Direct Protein-SIF (stable carbon isotope fingerprinting proteomics)