PXD009027

PXD009027 is an original dataset announced via ProteomeXchange.

Title	A crude-MS strategy for in-depth proteome analysis of the methane-oxidizing Methylocystis sp. strain SC2
Description	Using recent developments in sample preparation strategies and improvements in mass spectrometry (MS), an optimized procedure was developed to characterize the proteome of Methylocystis sp. strain SC2, a type II methanotroph. It represents one of the ecologically important groups of methane-oxidizing bacteria. The major challenge for developing an efficient analytical proteomics workflow for methanotrophic bacteria is the high amount of membrane-associated proteins that need to be efficiently solubilized and digested for downstream analysis. Therefore, each step of the workflow, including cell lysis, protein solubilization and digestion, and MS peptide quantification, was assessed and optimized. Our novel crude-lysate-MS approach proved to increase protein quantification accuracy and the proteome coverage of strain SC2. It captured 62% of predicted SC2 proteome, with 10-fold increase in membrane-associated proteins relative to less effective conditions. Use of crude cell lysate for downstream analysis showed not only to be highly efficient for strain SC2 but also for other members of the Methylocystaceae family. To validate the efficiency of our newly developed workflow, we analyzed the SC2 proteome under two contrasting nitrogen conditions, with a focus on the differential expression of proteins involved in methane and nitrogen metabolisms.
HostingRepository	PRIDE
AnnounceDate	2018-07-23
AnnouncementXML	Submission_2018-07-23_08:33:54.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Timo Glatter
SpeciesList	scientific name: Lasionycta albinuda; NCBI TaxID: 716714; scientific name: Methylocystis sp. SC2; NCBI TaxID: 187303;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-23 06:00:08	ID requested
⏵ 1	2018-07-23 08:33:55	announced

Hakobyan A, Liesack W, Glatter T, Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2. J Proteome Res, 17(9):3086-3103(2018) [pubmed]

curator keyword: Biological

submitter keyword: Label-free quantification, Bacterial proteomics, Methane Oxidation, Sample preparation

Timo Glatter
contact affiliation	Max-Planck Institute for terrestrial Microbiology
contact email	glatter@mpi-marburg.mpg.de
lab head
Timo Glatter
contact affiliation	MPI Marburg
contact email	glatter@mpi-marburg.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD009027
     1. Label: PRIDE project
     2. Name: A crude-MS strategy for in-depth proteome analysis of the methane-oxidizing Methylocystis sp. strain SC2