ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

Mooradian, Arshag D.; Post, Sjoerd van der; Naegle, Kristen M.; Held, Jason M.

doi:10.1371/journal.pcbi.1007741

Cited by 16 publications

(17 citation statements)

References 17 publications

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“…The pipeline proposed in this study allows discriminating host, residual food, and microbiome proteins, and identifies the main taxa and their functions at an unprecedented range, including archaea, bacteria, fungi, and parasites. This approach gives more flexibility in database construction, cascade layout, and parameter optimization than currently available tools such as Unipept 5 , MetaLab 15 , MPA 30 , or ProteoClade 31 , which have not been specifically conceived for the analysis of microbiomes from nonsequenced hosts. We believe this strategy can be of great value for future microbiome studies of numerous non-model animals, providing a valid alternative for studies in diverse areas such as environmental biomonitoring, aquaculture, parasitology, or biocontrol.…”

Section: Psm Fdr 1%mentioning

confidence: 99%

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host

Gouveia

Pible

Culotta

et al. 2020

npj Biofilms Microbiomes

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Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.

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Section: Psm Fdr 1%mentioning

confidence: 99%

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host

Gouveia

Pible

Culotta

et al. 2020

npj Biofilms Microbiomes

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“…A target FDR of 0.01 was used to filter PSMs and peptides. Proteoclade was utilized to annotate peptides belonging to human, mouse, or shared; filter for Homo sapiens specific peptides; and recalculate protein abundances from the sum of only human-unique peptides. Mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD035070.…”

Section: Methodsmentioning

confidence: 99%

Subgroup-Enriched Pathways and Kinase Signatures in Medulloblastoma Patient-Derived Xenografts

et al. 2022

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Medulloblastoma (MB) is the most common malignant pediatric brain tumor. MB is classified into four primary molecular subgroups: wingless (WNT), sonic hedgehog (SHH), Group 3 (G3), and Group 4 (G4), and further genomic and proteomic subtypes have been reported. Subgroup heterogeneity and few actionable mutations have hindered the development of targeted therapies, especially for G3 MB, which has a particularly poor prognosis. To identify novel therapeutic targets for MB, we performed mass spectrometry-based deep expression proteomics and phosphoproteomics in 20 orthotopic patient-derived xenograft (PDX) models of MB comprising SHH, G3, and G4 subgroups. We found that the proteomic profiles of MB PDX tumors are closely aligned with those of primary human MB tumors illustrating the utility of PDX models. SHH PDXs were enriched for NFκB and p38 MAPK signaling, while G3 PDXs were characterized by MYC activity. Additionally, we found a significant association between actinomycin D sensitivity and increased abundance of MYC and MYC target genes. Our results highlight several candidate pathways that may serve as targets for new MB therapies. Mass spectrometry data are available via ProteomeXchange with identifier PXD035070.

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“…The proteins of the same group usually exhibit the same function but have different taxonomic origins; therefore, the taxonomic origin of the entire protein group can be described by the lowest common ancestor within a phylogenetic tree [48] . Other methods for taxonomical annotation of metaproteomic data include the use of taxon-specific peptides, such as UniPep and ProteoClade [90] , [91] .…”

Section: Current Challenges Of Stool-based Metaproteomicsmentioning

confidence: 99%

Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics

Pettersen

Antunes

Dufour

et al. 2022

Computational and Structural Biotechnology Journal

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Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography–mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.

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ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

Cited by 16 publications

References 17 publications

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host

Subgroup-Enriched Pathways and Kinase Signatures in Medulloblastoma Patient-Derived Xenografts

Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics

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