Proteomics

Dataset Information

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LineageFilter: Estimating the taxonomic composition of complex samples using metaproteomics and machine learning

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Enterococcus Faecalis (streptococcus Faecalis) Acinetobacter Baumannii Limosilactobacillus Fermentum Streptoccous Pyogenes Viruses Candida Albicans (yeast) Salmonella Enterica Bacillus Subtilis Saccharomyces Cerevisiae (baker's Yeast) Cellulomonas Hominis Klebsiella Pneumoniae Bacteroides Thetaiotaomicron Clostridium Butyricum Cryptococcus Neoformans Escherichia Coli Bifidobacterium Longum Lactobacillus Plantarum Bacteria Staphylococcus Aureus Enterococcus Faecium Thomasclavelia Ramosa Listeria Monocytogenes Pseudomonas Aeruginosa Eukaryota (eucaryotes) Blautia Producta Anaerostipes Caccae

SUBMITTER: Jean ARMENGAUD  

LAB HEAD: Jean Armengaud

PROVIDER: PXD049349 | Pride | 2024-11-06

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
Candida_MiniMix100.mgf Mgf
F400284.dat Other
F400284_p0.05.mzid.gz Mzid
F405583.dat Other
F405583_p0.05.mzid.gz Mzid
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Publications

LineageFilter: Improved Proteotyping of Complex Samples Using Metaproteomics and Machine Learning.

Hachemi Hamid H   Armengaud Jean J   Grenga Lucia L   Pible Olivier O  

Journal of proteome research 20241019 11

Metaproteomics is a powerful tool to characterize how microbiota function by analyzing their proteic content by tandem mass spectrometry. Given the complexity of these samples, accurately assessing their taxonomical composition without prior information based solely on peptide sequences remains a challenge. Here, we present LineageFilter, a new python-based AI software for refined proteotyping of complex samples using metaproteomics interpreted data and machine learning. Given a tentative list o  ...[more]

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