ProteoStorm: An Ultrafast Metaproteomics Database Search Framework

Beyter, Doruk; Lin, Miin S.; Yu, Yonghao; Pieper, Rembert; Bafna, Vineet

doi:10.1016/j.cels.2018.08.009

Cited by 35 publications

(26 citation statements)

References 26 publications

(42 reference statements)

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“…Shotgun metaproteomics may uncover the functional geography of microbial population, but needs suitable strategies for complicated tests with obscure formulations. Beyter et al [84] have displayed Proteo-Storm, a competitive database looks like a framework for large-scale metaproteomics that identifies high-confidence peptidespectrum matches while accomplishing a speedup of two-to-three orders-of-magnitude over reigning systems. Metaproteomics could be an effective tool for getting information on all proteins recuperated specifically from natural tests at a given time.…”

Section: Metaproteomicsmentioning

confidence: 99%

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

et al. 2020

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The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.

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Section: Metaproteomicsmentioning

confidence: 99%

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

et al. 2020

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“…For protein identification, bottom‐up metaproteomics requires taxonomy‐specific peptides for microbial community identification, quantification, functional annotation, and biological classification or metabolic analysis (Zhang & Figeys, 2019b). Several bioinformatics analysis software and platforms are available, such as Unipept (Gurdeep Singh et al., 2019), MetaLab (Cheng et al., 2017), ProteoStorm (Beyter, Lin, Yu, Pieper, & Bafna, 2018), and Galaxy (Jagtap et al., 2015). Commonly used functional information databases include Cluster of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG).…”

Section: Metaproteomics Analysis Methodsmentioning

confidence: 99%

Metaproteomics insights into traditional fermented foods and beverages

Yang

Fan

2020

Comp Rev Food Sci Food Safe

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Traditional fermented foods and beverages (TFFB) are important dietary components. Multi‐omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi‐omics technology requires further integration to reveal the molecular nature of TFFB fermentation.

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“…The other challenge of metaproteomic database searches is the large computational workload and low sensitivity attributed to the large size of microbiome databases. An efficient approach to dealing with this challenge is iterative database search strategies, which first reduces the original database by searching a target‐limited database or simplifying the database search parameters . The refined database will be used for the second or third database searches for increased sensitivity and accuracy of peptide identifications.…”

Section: Investigating the Gut Microbiome With Metaproteomicsmentioning

confidence: 99%

Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome

et al. 2019

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The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signaling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases are reviewed.Samples collected from the human gut contains microbiome and host proteins. These microbiome/host proteins directly represent the functional activity of the intestinal ecosystem and can be simultaneously measured by metaproteomics. Metaproteomics can also provide valuable information on the pathways and taxaspecific functions, which provides a more in-depth perspective for studying detailed mechanisms underlying host-microbiome

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ProteoStorm: An Ultrafast Metaproteomics Database Search Framework

Cited by 35 publications

References 26 publications

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

RETRACTED ARTICLE: Metagenomics for taxonomy profiling: tools and approaches

Metaproteomics insights into traditional fermented foods and beverages

Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome

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