PXD003028

PXD003028 is an original dataset announced via ProteomeXchange.

Title	Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome
Description	The oral cavity is home to one of the most diverse microbial community of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions including lubrication of food, predigesting and bacterial defense. Consequently, disruptions in saliva secretion contributes to conditions such as tooth decay and respiratory tract infections. Here we used recent improvements in mass spectrometry (MS)-based proteomics to develop a rapid workflow for mapping to map the saliva proteome quantitatively and at great depth. Microgram protein amounts retrieved from cotton swabs were processed in a single-run format, resulting in more than 3,700 quantified human proteins in 100 min measurements gradients. After separation into eight fractions, this increased to 5,500 human proteins. Remarkably, our measurements also quantified more than 2,000 microbial proteins and we find peptide evidence for more than 70 bacterial genera without any microbial culture. Co-analysis of the proteomics results with next generation sequencing data as well as MALDI Biotyper revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing. Rapid and robust shotgun technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:26:11.002.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Niklas Grassl
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-10-09 07:59:18	ID requested
1	2016-03-18 10:51:28	announced
2	2016-04-25 03:31:09	announced	Updated publication reference for PubMed record(s): 27102203.
⏵ 3	2024-10-22 04:26:19	announced	2024-10-22: Updated project metadata.

10.1186/s13073-016-0293-0;

Grassl N, Kulak NA, Pichler G, Geyer PE, Jung J, Schubert S, Sinitcyn P, Cox J, Mann M, Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome. Genome Med, 8(1):44(2016) [pubmed]

curator keyword: Biological

submitter keyword: saliva, bRP, microbiome, metaproteome, NGS, MS, plasma, blood, fractionation, biomarker

Matthias Mann
contact affiliation	Department of proteomics and signal transduction, max planck institute of biochemistry, Germany
contact email	mmann@biochem.mpg.de
lab head
Niklas Grassl
contact affiliation	Max-Planck Institute of Biochemistry
contact email	grassl@biochem.mpg.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/2016/03/PXD003028

PRIDE project URI

• PRIDE
  1. PXD003028
     1. Label: PRIDE project
     2. Name: Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome