Dataset Information

A crude-MS strategy for in-depth proteome analysis of the methane-oxidizing Methylocystis sp. strain SC2

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Lasionycta Albinuda Methylocystis Sp. Sc2

TISSUE(S): Cell Culture

SUBMITTER: Timo Glatter

LAB HEAD: Timo Glatter

PROVIDER: PXD009027 | Pride | 2018-07-23

REPOSITORIES: Pride

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Publications

Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2.

Hakobyan Anna A Liesack Werner W Glatter Timo T

Journal of proteome research 20180808 9

Methylocystis sp. strain SC2 is a representative of the alphaproteobacterial methane oxidizers or type IIa methanotrophs. These microorganisms play a crucial role in methane cycling. Here, we developed an efficient analytical proteomics workflow for strain SC2. It tackles the major challenges related to the high amount of integral membrane proteins that need to be efficiently solubilized and digested for downstream analysis. Each step of the workflow, including cell lysis, protein solubilization ...[more]

PMID: 30019905

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Dataset Information

A crude-MS strategy for in-depth proteome analysis of the methane-oxidizing Methylocystis sp. strain SC2

Publications

Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2.

Similar Datasets

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