PXD026727

PXD026727 is an original dataset announced via ProteomeXchange.

Title	Free-Flow Isoelectric Focusing Based Metaproteomics Workflow Facilitates the Identification and Characterization of Human Salivary Microbiome for Lung Cancer
Description	We developed a free-flow isoelectric focusing (FFIEF) based metaproteomics workflow to reduce the host interferences and enrich the low-abundant bacteria for better interpretation of salivary microbiome. We firstly tested the pretreatment module that could significantly reduce the host interferences by differential centrifugation and filtration. Then the FFIEF module was applied to separate the microbes and enrich the low-abundant bacteria, which showed a significant improvement in the identification efficiency of microbiome sample. Applying our method to lung cancer, we successfully identified Fusobacterium, Neisseriaceae, Actinomycetaceae, Burkholderiales, and Spirochaetia were associated with lung cancer as previous sequencing studies did, along with other 16 significantly different species. The dysregulated functions in lung cancer microbiome were also explained in details. Our workflow provides improved efficiency in identification and characterization of the salivary microbiome with great reproducibility. The ability of enriching low-abundant bacteria and functions enables in-deep analysis of previously underestimated information.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:50:31.025.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	xiaoteng Jiang
SpeciesList	scientific name: human saliva metagenome; NCBI TaxID: 1679718;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-15 14:42:52	ID requested
1	2022-11-17 06:59:08	announced
⏵ 2	2023-11-14 07:50:34	announced	2023-11-14: Updated project metadata.

Jiang X, Zhang Y, Wang H, Wang Z, Hu S, Cao C, Xiao H, In-Depth Metaproteomics Analysis of Oral Microbiome for Lung Cancer. Research (Wash D C), 2022():9781578(2022) [pubmed]

submitter keyword: Taxonomy-function integration, Lung cancer, Metaproteomics,Free-flow isoelectric focusing, Salivary microbiome, Dysbiosis

Hua Xiao
contact affiliation	State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
contact email	huaxiao@sjtu.edu.cn
lab head
xiaoteng Jiang
contact affiliation	Shanghai Jiao Tong University, SJTU
contact email	jiang.xiaoteng@sjtu.edu.cn
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/2022/11/PXD026727

PRIDE project URI

• PRIDE
  1. PXD026727
     1. Label: PRIDE project
     2. Name: Free-Flow Isoelectric Focusing Based Metaproteomics Workflow Facilitates the Identification and Characterization of Human Salivary Microbiome for Lung Cancer