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PXD027306

PXD027306 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA Metaproteomic Workflow for Sample Preparation and Data Analysis Applied to Mouse Faeces: 5
DescriptionThe intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behaviour. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomic is well suited for analysis of individual microbes, metaproteomic of faecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of species. Furthermore, there is a lack of consensus regarding preparation of faecal samples, as well as downstream bioinformatic analyses following metaproteomic data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse faeces in a typical LC-MS/MS metaproteomic experiment. We show that low speed centrifugation (LSC) of faecal samples leads to high protein identification rates but possibly enriched for a subset of taxa. During database search, two-step search strategies led to dramatic and underestimated accumulation of false positive protein identifications. Regarding taxonomic annotation, the MS-identified peptides of unknown origin were annotated with highest sensitivity and specificity using the Unipept software. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomic when studying complex microbiome samples.
HostingRepositoryPRIDE
AnnounceDate2022-02-17
AnnouncementXMLSubmission_2022-02-17_05:27:42.089.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterNicolas Nalpas
SpeciesList scientific name: Archaea; NCBI TaxID: 2157; scientific name: Viruses; NCBI TaxID: 10239; scientific name: Eukaryota; NCBI TaxID: 2759; scientific name: Bacteria; NCBI TaxID: 2;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-07-14 07:37:37ID requested
12022-02-17 05:27:43announced
Publication List
Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas ME, Macek B, An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. Gut Microbes, 13(1):1994836(2021) [pubmed]
Keyword List
submitter keyword: Metaproteomics, Mus musculus, Metagenome, Taxonomy
Contact List
Prof. Dr. Boris Macek
contact affiliationQuantitative Proteomics Proteome Center Tübingen Universität Tübingen Auf der Morgenstelle 15 72076 Tübingen
contact emailboris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliationTuebingen University
contact emailnalpas.nicolas@gmail.com
dataset submitter
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Dataset FTP location
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PRIDE project URI
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