Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions

Starr, Amanda E.; Deeke, Shelley A.; Li, Leyuan; Zhang, Xu; Daoud, Rachid; Ryan, James W.; Ning, Zhibin; Cheng, Kai; Nguyen, Linh Vu; Abou-Samra, Elias; Lavallée‐Adam, Mathieu; Figeys, Daniel

doi:10.1021/acs.analchem.7b04340

Cited by 48 publications

(44 citation statements)

References 278 publications

(497 reference statements)

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“…It functions on all major operating systems and operates at a speed and scale that enable fast and novel forms of proteomic data processing using consumer hardware. Proteo-Clade's ease of use, applicability to a broad set of biological model systems such as PDXs and metaproteomics, and its novel integration with de novo spectral searches [4] provides a unique and powerful tool to researchers performing quantitative proteomic analysis of multiple mixed species.…”

Section: Plos Computational Biologymentioning

confidence: 99%

“…These studies universally perform bottom-up analysis, where proteins are digested into peptides with a protease, and therefore require assignment of peptides to proteins based on their taxonomic specificity. Several software tools provide one or more of these features, but have practical and technical limitations that render them unable to facilitate complete analysis pipelines of quantitative proteomics data and scale to the rapidly increasing number of available reference protein sequences [4,5]. With regard to annotating peptides to taxa, Unipept is a commonly used taxonomic annotation tool that can provide access to the entire UniProt sequence repository, provides web-based visualizations and a command line interface, and was demonstrated to annotate peptides orders of magnitude faster than a prior UniProt-based application, Peptide Match [6,7].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patientderived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples.

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Section: Plos Computational Biologymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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“…There are considerable technical challenges resulting in part from the complexity arising from studying, in effect, multiple species from the same sample: hundreds of bacterial species may be present in varying amounts within the clinical sample. Considerable progress has been made, as reviewed by Starr et al [190]. A key development in proteomic tools includes the stable isotopically labelled microbiota (SILAMi) technique to study intestinal metaproteomes [191] and the MetaPro-IQ database for high-efficiency protein identifications of gut microbiome samples [192].…”

Section: Future Perspectivesmentioning

confidence: 99%

Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives

Assadsangabi

Evans

Corfe

et al. 2019

Gastroenterology Research and Practice

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Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date. This is because the presence of a given gene mutation does not automatically correspond to changes in its expression or final metabolic or structural effect(s). Furthermore, the existence of these gene susceptibility loci in the normal population suggests other driving prerequisites for the disease manifestation. Proteins can be considered the main functional units as almost all intracellular physiological functions as well as intercellular interactions are dependent on them. Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved. Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression. This review describes the state of the art in the field with respect to the study of IBD and the potential for translation from biomarker discovery to clinical application.

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“…These studies universally perform bottom-up analysis, where proteins are digested into peptides with a protease, and therefore require assignment of peptides to proteins based on their taxonomic specificity. Several software tools provide one or more of these features, but have practical and technical limitations that render them unable to facilitate complete analysis pipelines of quantitative proteomics data and scale to the rapidly increasing number of available reference protein sequences 4,5 . With regard to annotating peptides to taxa, Unipept is a commonly used taxonomic annotation tool that can provide access to the entire UniProt sequence repository, provides web-based visualizations and a command line interface, and was demonstrated to annotate peptides orders of magnitude faster than a prior UniProt-based application, Peptide Match 6,7 .…”

Section: Main Textmentioning

confidence: 99%

“…It functions on all major operating systems and operates at a speed and scale that enable fast and novel forms of proteomic data processing using consumer hardware. We expect ProteoClade’s ease of use, applicability to a broad set of biological model systems such as PDXs and metaproteomics, and its novel integration with de novo spectral searches 4 provides a unique and powerful tool to researchers performing quantitative proteomic analysis of multiple mixed species.…”

Section: Main Textmentioning

confidence: 99%

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

Mooradian

Post

Naegle

et al. 2019

Preprint

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15We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein infer-16 ence, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of 17 millions of protein sequences, requires minimal computational resources, and is open source, multi-18 platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative 19 proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de 20 novo proteomic workflow for complex microbiota samples. 21 22Main Text: 23The goal of metaproteomic and multispecies proteomic studies is to characterize the proteomes of sam-24 ples containing multiple, comingled species, which can provide insight into the complex interactions at 25 the interface between organisms. Proteomic analysis of these samples can quantify thousands of pro-26 teins from hundreds of species in a single mass spectrometry experiment 1 , characterize education of 27 stromal tissue by patient-derived xenografts (PDXs) 2 , and extensively characterize the human oral mi-28 crobiome 3 . 29Metaproteomic and multispecies data analyses depend on the ability to integrate reference protein se-30 quence databases, taxonomic lineages, in silico proteolytic digestion, peptide identification, and quanti-31 tation. These studies universally perform bottom-up analysis, where proteins are digested into peptides 32 with a protease, and therefore require assignment of peptides to proteins based on their taxonomic 33 specificity. Several software tools provide one or more of these features, but have practical and tech-34 nical limitations that render them unable to facilitate complete analysis pipelines of quantitative prote-35 omics data and scale to the rapidly increasing number of available reference protein sequences 4,5 . With 36 regard to annotating peptides to taxa, Unipept is a commonly used taxonomic annotation tool that can 37 provide access to the entire UniProt sequence repository, provides web-based visualizations and a

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Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions

Cited by 48 publications

References 278 publications

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

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

Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives

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

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