PXD014272

PXD014272 is an original dataset announced via ProteomeXchange.

Title	Ariadne’s Thread in the Analytical Labyrinth of Membrane Proteins – Integration of Targeted and Shotgun Proteomics for Global Absolute Quantification of Membrane Proteins
Description	The field of systems biology has been rapidly increasing in the past decade. However, the data produced by “omics” approaches is lagging behind the requirements of this field, especially when it comes to absolute abundances of membrane proteins. In the present study, a novel approach for large-scale absolute quantification of this challenging subset of proteins has been established and evaluated using osmotic stress management in the Gram-positive model bacterium Bacillus subtilis as proof of principle precedent. Selected membrane proteins were labelled using a SNAP-tag, which allowed to visually inspect the enrichment of the membrane fraction by immunoassays. Absolute membrane protein concentrations were determined via shotgun proteomics by spiking crude membrane extracts of chromosomally SNAP-tagged and wild-type B. subtilis strains with protein standards of known concentration. Shotgun data was subsequently calibrated by targeted mass spectrometry using SNAP as an anchor protein, and an enrichment factor was calculated in order to obtain membrane protein copy numbers/µm2. The presented approach enabled the accurate determination of physiological changes resulting from imposed hyperosmotic stress, thereby offering a clear visualization of alterations in membrane protein arrangements and shedding light on putative membrane complexes. This straightforward and cost-effective methodology for quantitative proteome studies can be implemented by any research group with mass-spectrometry expertise. Importantly, it can be applied to the full spectrum of physiologically relevant conditions, ranging from environmental stresses to the biotechnological production of small molecules and proteins, which relies heavily on B. subtilis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:55:53.293.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Minia Antelo
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationList	iodoacetamide derivatized residue
Instrument	TSQ Vantage; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-17 02:44:36	ID requested
1	2019-08-26 00:49:27	announced
⏵ 2	2024-10-22 04:55:54	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.9b02869;

Antelo-Varela M, Bartel J, Quesada-Ganuza A, Appel K, Bernal-Cabas M, Sura T, Otto A, Rasmussen M, van Dijl JM, Nielsen A, Maa, ß S, Becher D, Ariadne's Thread in the Analytical Labyrinth of Membrane Proteins: Integration of Targeted and Shotgun Proteomics for Global Absolute Quantification of Membrane Proteins. Anal Chem, 91(18):11972-11980(2019) [pubmed]

submitter keyword: Shotgun-MS, Absolute Quantification, Targeted-MS, SNAP-tag, Bacillus subtilis,Membrane proteins

Dörte Becher
contact affiliation	University of Greifswald Center of Functional Genomics of Microbes Institute of Microbiology Department of Microbial Proteomics Felix-Hausdorff-Str.8 17489 Greifswald phone: +49 3834 420 5903 fax: +49 3834 420 5902
contact email	dbecher@uni-greifswald.de
lab head
Minia Antelo
contact affiliation	Institute of Microbiology University of Greifswald
contact email	minia.antelovarela@uni-greifswald.de
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/2019/08/PXD014272

PRIDE project URI

• PRIDE
  1. PXD014272
     1. Label: PRIDE project
     2. Name: Ariadne’s Thread in the Analytical Labyrinth of Membrane Proteins – Integration of Targeted and Shotgun Proteomics for Global Absolute Quantification of Membrane Proteins