PXD004041

PXD004041 is an original dataset announced via ProteomeXchange.

Title	An omics-based metabolic model of methane-driven denitrification by aerobic methanotrophic bacteria
Description	Methylomonas denitrificans is the first characterized organism that couples methane oxidation to nitrate reduction in pure culture without a partner. The aim of this study is to develop a metabolic model of methane driven nitrate respiration using a multi-level omics approach. Samples of M. denitrificans biomass were harvested during growth at high and limiting oxygen and whole transcriptome/proteome analyses were carried out on samples from both conditions. Comparative analysis of transcript and protein abundance between the two conditions was used to develop a metabolic model of methane driven nitrate respiration. 1. Wisniewski JR, Zougman A, Nagaraj N, Mann M: Universal sample preparation method for proteome analysis. Nat Meth 2009, 6:359-362. 2. Oberg AL, Vitek O: Statistical design of quantitative mass spectrometry-based proteomic experiments. J Proteome Res 2009, 8:2144-2156. 3. Olsen JV, de Godoy LMF, Li G, Macek B, Mortensen P, Pesch R, Makarov A, Lange O, Horning S, Mann M: Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 2005, 4:2010-2021.
HostingRepository	PRIDE
AnnounceDate	2025-09-17
AnnouncementXML	Submission_2025-09-17_09:55:18.011.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Kleiner
SpeciesList	scientific name: Methylomonas denitrificans; NCBI TaxID: 1538553;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-25 01:17:14	ID requested
⏵ 1	2025-09-17 09:55:18	announced

10.1128/MBIO.01533-25;

curator keyword: Biological

submitter keyword: Methane, denitrification, omics, hypoxic, Methylomonas, respiration, methanotroph, nitrous oxide, nitrate

Manuel Kleiner
contact affiliation	University of Calgary, Department of Geoscience
contact email	manuel.kleiner@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/2025/09/PXD004041

PRIDE project URI

• PRIDE
  1. PXD004041
     1. Label: PRIDE project
     2. Name: An omics-based metabolic model of methane-driven denitrification by aerobic methanotrophic bacteria