PXD009027 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-02-23 06:00:08 | ID requested | |
⏵ 1 | 2018-07-23 08:33:55 | announced | |
Publication List
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] |
Keyword List
curator keyword: Biological |
submitter keyword: Label-free quantification, Bacterial proteomics, Methane Oxidation, Sample preparation |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD009027
- Label: PRIDE project
- Name: A crude-MS strategy for in-depth proteome analysis of the methane-oxidizing Methylocystis sp. strain SC2