PXD003176

PXD003176 is an original dataset announced via ProteomeXchange.

Title	Unique insights in cervicovaginal Lactobacillus iners and L. crispatus proteome changes associated with microbiome dysbiosis
Description	Cervicovaginal lavage (CVL)supernatants were heat inactivated for 30 minutes at 56°C before further processing. Total protein concentrations were determined using the Pierce Coomassie Plus (Bradford) Protein Assay (Thermo Scientific, Rockford, IL, USA). Sample protein content and volume were normalised with 25mM ammonium bicarbonate (ABC). Soluble proteins were precipitated using an equal volume of ice cold 30% (w/v) TCA in acetone and incubated at -20⁰C for 2 hours. Samples were centrifuged at 12,000g for 10 minutes (4⁰C) to pellet proteins. Pellets were washed three times with ice cold acetone and allowed to air dry. Further sample processing was performed as previously described (Armstrong et al, 2014) with minor modifications. Briefly, protein pellets were resuspended in 25 mM ABC, 0.05%(w/v) rapigest (Waters), reduced and alkylated. Digestion was performed with proteomic-grade trypsin (Sigma-Aldrich, St. Louis, MO, USA) at a protein:trypsin ratio of 50:1. Rapigest was precipitated by addition of trifluoroacetic acid to a final concentration of 0.5% (v/v). Peptide mixtures were analyzed by on-line nanoflow liquid chromatography using the nanoACQUITY-nLC system (Waters MS technologies) coupled to an LTQ-Orbitrap Velos (ThermoFisher Scientific, Bremen, Germany) mass spectrometer equipped with the manufacturer’s nanospray ion source. The gradient of the analytic column (nanoACQUITY UPLCTM BEH130 C18 15cm x 75µm, 1.7µm capillary column) consisted of 3-40% acetonitrile in 0.1% formic acid for 90 min then a ramp of 40-85% acetonitrile in 0.1% formic acid for 5min.
HostingRepository	PRIDE
AnnounceDate	2016-03-15
AnnouncementXML	Submission_2016-03-14_17:51:37.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD003176
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stuart Armstrong
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Lactobacillus crispatus; NCBI TaxID: 47770; scientific name: Lactobacillus iners; NCBI TaxID: 147802;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-11-11 05:57:17	ID requested
⏵ 1	2016-03-14 17:51:38	announced

Borgdorff H, Armstrong SD, Tytgat HL, Xia D, Ndayisaba GF, Wastling JM, van de Wijgert JH, Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis. PLoS One, 11(3):e0150767(2016) [pubmed]

submitter keyword: cervicovaginal microbiome dysbiosis, label free proteomics

Julian Hiscox
contact affiliation	Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool. Liverpool, L3 5RF, UK.
contact email	julianh@liverpool.ac.uk
lab head
Stuart Armstrong
contact affiliation	Infection Biology
contact email	sarmstro@liv.ac.uk
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/2016/03/PXD003176

PRIDE project URI

• PRIDE
  1. PXD003176
     1. Label: PRIDE project
     2. Name: Unique insights in cervicovaginal Lactobacillus iners and L. crispatus proteome changes associated with microbiome dysbiosis