PXD050781

PXD050781 is an original dataset announced via ProteomeXchange.

Title	Spectral entropy as a measure of the metaproteome complexity
Description	The diversity and complexity of the microbiome's genomic landscape are not always mirrored in its proteomic profile. Despite the anticipated proteomic diversity, observed complexities of microbiome sample are often lower than expected. Two main factors contribute to this discrepancy: limitations in mass spectrometry's detection sensitivity and bioinformatics challenges in metaproteomics identification. This study introduces a novel approach to evaluating sample complexity directly at the full mass spectrum (MS1) level rather than relying on peptide identifications. When analyzing under identical mass spectrometry conditions, microbiome samples displayed significantly higher complexity, as evidenced by the spectral entropy and peptide candidate entropy, compared to single-species samples. The research provides solid evidence for the complexity of microbiome in proteomics indicating the optimization potential of the bioinformatics workflow.
HostingRepository	PRIDE
AnnounceDate	2024-05-27
AnnouncementXML	Submission_2024-05-27_12:57:04.546.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Haonan Duan
SpeciesList	scientific name: gut metagenome; NCBI TaxID: 749906;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-19 13:23:35	ID requested
⏵ 1	2024-05-27 12:57:05	announced

10.1002/pmic.202300570;

Duan H, Ning Z, Zhang A, Figeys D, Spectral entropy as a measure of the metaproteome complexity. Proteomics, 24(16):e2300570(2024) [pubmed]

submitter keyword: bioinformatics, spectral entropy, metaproteomics

Daniel Figeys
contact affiliation	Director and Professor, School of Pharmaceutical Sciences
contact email	dfigeys@uottawa.ca
lab head
Haonan Duan
contact affiliation	School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
contact email	hduan084@uottawa.ca
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/2024/05/PXD050781

PRIDE project URI

• PRIDE
  1. PXD050781
     1. Label: PRIDE project
     2. Name: Spectral entropy as a measure of the metaproteome complexity