PXD007510

PXD007510 is an original dataset announced via ProteomeXchange.

Title	Metaproteomics of the marine gutless oligochaete Olavius algarvensis and its symbionts to determine stable isotope fingerprints using Direct Protein-SIF
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”. We validated and tested the method extensively using pure cultures (PXD006762) and mock communities (PXD006118, https://www.ebi.ac.uk/pride/archive/projects/PXD006118). As a case study we applied Direct Protein-SIF to the Olavius algarvensis symbiosis. Olavius algarvensis is a marine worm that lives in shallow-water sediments off the coast of Elba, Italy. The worm has no digestive and excretory system, instead it harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (http://www.pnas.org/content/109/19/E1173.short). For this project we generated metaproteomes of 14 O. algarvensis individuals. A total of 18 LC-MS/MS runs were generated. For Direct Protein-SIF the data from all runs was combined. In this submission we are including the Direct Protein-SIF specific isotope pattern file as well as the .mzML files and PSM file required as input for the Direct Protein-SIF software (Calis-p). In addition to the Olavius algarvensis samples a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are available through project PXD006762 (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_07:41:19.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Kleiner
SpeciesList	scientific name: Olavius algarvensis Gamma 1 endosymbiont; NCBI TaxID: 260705; scientific name: Chromatiales bacterium OalgGamma1; NCBI TaxID: 1123869; scientific name: Olavius algarvensis Gamma 3 endosymbiont; NCBI TaxID: 260704; scientific name: Spirochaeta sp. ELBA; NCBI TaxID: 1117957; scientific name: Olavius algarvensis; NCBI TaxID: 188229; scientific name: Olavius algarvensis Delta 1 endosymbiont; NCBI TaxID: 334747; scientific name: Olavius algarvensis Delta 4 endosymbiont; NCBI TaxID: 260707;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-17 23:56:20	ID requested
1	2018-05-21 02:34:27	announced
⏵ 2	2019-02-18 07:41:20	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, metaproteome, symbiosis, symbiont

Manuel Kleiner
contact affiliation	North Carolina State University at Raleigh
contact email	manuel_kleiner@ncsu.edu
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/PXD007510

PRIDE project URI

• PRIDE
  1. PXD007510
     1. Label: PRIDE project
     2. Name: Metaproteomics of the marine gutless oligochaete Olavius algarvensis and its symbionts to determine stable isotope fingerprints using Direct Protein-SIF