PXD049349

PXD049349 is an original dataset announced via ProteomeXchange.

Title	LineageFilter: Estimating the taxonomic composition of complex samples using metaproteomics and machine learning
Description	In this study we developped LineageFilter, a new method for refined proteotyping of complex samples using metaproteomics raw data and machine learning. Given a tentative list of taxa, their abundance, and the scores associated to their identified peptides, LineageFilter computes a comprehensive set of features for each identified taxon at all taxonomical ranks. Its machine-learning model assesses the likelihood of each taxon's presence based on these features, enabling efficient filtration of false-positive taxa.
HostingRepository	PRIDE
AnnounceDate	2024-11-06
AnnouncementXML	Submission_2024-11-06_02:27:30.937.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD049349
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jean ARMENGAUD
SpeciesList	scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Streptoccous pyogenes; NCBI TaxID: 1314; scientific name: Limosilactobacillus fermentum; NCBI TaxID: 1613; scientific name: Pseudomonas aeruginosa; NCBI TaxID: 287; scientific name: Enterococcus faecalis (Streptococcus faecalis); NCBI TaxID: 1351; scientific name: Bifidobacterium longum; NCBI TaxID: 216816; scientific name: Bacillus subtilis; NCBI TaxID: 1423; scientific name: Eukaryota (eucaryotes); NCBI TaxID: 2759; scientific name: Enterococcus faecium; NCBI TaxID: 1352; scientific name: Acinetobacter baumannii; NCBI TaxID: 470; scientific name: Clostridium butyricum; NCBI TaxID: 1492; scientific name: Listeria monocytogenes; NCBI TaxID: 1639; scientific name: Viruses; NCBI TaxID: 10239; scientific name: Cryptococcus neoformans; NCBI TaxID: 5207; scientific name: Staphylococcus aureus; NCBI TaxID: 1280; scientific name: Anaerostipes caccae; NCBI TaxID: 105841; scientific name: Thomasclavelia ramosa; NCBI TaxID: 1547; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; scientific name: Bacteria; NCBI TaxID: 2; scientific name: Cellulomonas hominis; NCBI TaxID: 156981; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Klebsiella pneumoniae; NCBI TaxID: 573; scientific name: Blautia producta; NCBI TaxID: 33035; scientific name: Bacteroides thetaiotaomicron; NCBI TaxID: 818; scientific name: Lactobacillus plantarum; NCBI TaxID: 1590; scientific name: Salmonella enterica; NCBI TaxID: 28901;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-13 02:19:01	ID requested
⏵ 1	2024-11-06 02:27:31	announced

10.1021/acs.jproteome.4c00184;

Hachemi H, Armengaud J, Grenga L, Pible O, LineageFilter: Improved Proteotyping of Complex Samples Using Metaproteomics and Machine Learning. J Proteome Res, 23(11):5203-5208(2024) [pubmed]

10.6019/PXD049349;

submitter keyword: proteomics, bioinformatics

Jean Armengaud
contact affiliation	CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France
contact email	jean.armengaud@cea.fr
lab head
Jean ARMENGAUD
contact affiliation	Li2D
contact email	jean.armengaud@cea.fr
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/2024/11/PXD049349

PRIDE project URI

• PRIDE
  1. PXD049349
     1. Label: PRIDE project
     2. Name: LineageFilter: Estimating the taxonomic composition of complex samples using metaproteomics and machine learning