PXD009596

PXD009596 is an original dataset announced via ProteomeXchange.

Title	Human Pap test LC-MS/MS metaproteomics
Description	The human cervical-vaginal area contains proteins derived from microorganisms that may prevent or predispose women to gynecological conditions. The liquid Pap test fixative is an unexplored resource for analysis of microbial communities and the microbe-host interaction. Previously, we showed that the residual cell-free fixative from discarded Pap tests of healthy women could be used for mass spectrometry (MS) based proteomic identification of cervical-vaginal proteins. In this study, we reprocessed these MS raw data files for metaproteomic analysis to characterize the microbial community composition and function of microbial proteins in the cervical-vaginal region. This was accomplished by developing a customized protein sequence database encompassing microbes likely present in the vagina. High-mass accuracy data were searched against the protein FASTA database using a two-step search method within the Galaxy for proteomics platform. Data was analyzed by MEGAN6 (MetaGenomeAnalyzer) for phylogenetic and functional characterization. We identified over 300 unique peptides from a variety of bacterial phyla and Candida. Peptides corresponding to proteins involved in carbohydrate metabolism, oxidation-reduction, and transport were identified. By identifying microbial peptides in Pap test supernatants it may be possible to acquire a functional signature of these microbes, as well as detect specific proteins associated with cervical health and disease.
HostingRepository	PRIDE
AnnounceDate	2018-07-23
AnnouncementXML	Submission_2018-07-23_05:10:55.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kristin Boylan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-04-25 05:25:50	ID requested
⏵ 1	2018-07-23 05:10:56	announced

Afiuni-Zadeh S, Boylan KLM, Jagtap PD, Griffin TJ, Rudney JD, Peterson ML, Skubitz APN, Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome. Sci Rep, 8(1):10868(2018) [pubmed]

curator keyword: Metaproteomics

submitter keyword: Pap test, metaproteomics, microbiome

Amy P. N. Skubitz
contact affiliation	Professor, Department of Laboratory Medicine &Pathology Adjunct Professor, Department of Obstetrics, Gynecology& Women's Health Director, Ovarian Cancer Early Detection Program University of Minnesota Minneapolis, Minnesota, USA
contact email	skubi002@umn.edu
lab head
Kristin Boylan
contact affiliation	University of Minnesota
contact email	boyla002@umn.edu
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/2018/07/PXD009596

PRIDE project URI

• PRIDE
  1. PXD009596
     1. Label: PRIDE project
     2. Name: Human Pap test LC-MS/MS metaproteomics