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PXD003028

PXD003028 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleUltra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2016-03-18
AnnouncementXMLSubmission_2016-04-25_03:31:08.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterNiklas Grassl
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-10-09 07:59:18ID requested
12016-03-18 10:51:28announced
22016-04-25 03:31:09announcedUpdated publication reference for PubMed record(s): 27102203.
Publication List
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]
Keyword List
curator keyword: Biological
submitter keyword: saliva, microbiome, metaproteome, plasma, blood, fractionation, bRP, biomarker, MS, NGS
Contact List
Matthias Mann
contact affiliationDepartment of proteomics and signal transduction, max planck institute of biochemistry, Germany
contact emailmmann@biochem.mpg.de
lab head
Niklas Grassl
contact affiliationMax-Planck Institute of Biochemistry
contact emailgrassl@biochem.mpg.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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