+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis

Journal of Proteome Research 17(4): 1596-1605

Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 046280965

Download citation: RISBibTeXText

PMID: 29436230

DOI: 10.1021/acs.jproteome.7b00894

Related references

An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing. Journal of Proteome Research 15(8): 2697-2705, 2016

Analysis of human serum phosphopeptidome by a focused database searching strategy. Journal of Proteomics 78: 389-397, 2013

Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics 29(18): 2253-2260, 2013

Identification of anabolic steroids and derivatives using bioassay-guided fractionation, UHPLC/TOFMS analysis and accurate mass database searching. Analytica Chimica Acta 664(1): 77-88, 2010

A novel bioinformatics strategy for searching industrially useful genome resources from metagenomic sequence libraries. Genes and Genetic Systems 86(1): 53-66, 2011

Integrated metagenomic and metaproteomic analyses of marine biofilm communities. Biofouling 30(10): 1211-1223, 2014

Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis. Proteomics 11(6): 1075-1085, 2011

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm. Environmental Microbiology 18(1): 273-287, 2016

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. Isme Journal 6(9): 1688-1701, 2012

Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach. Water Science and Technology 67(7): 1650-1656, 2013

Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environmental Microbiology 14(5): 1333-1346, 2012

Novel strategy for database searching in spin liouville space by NMR ensemble computing. Physical Review Letters 85(22): 4815-4818, 2000

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. Environmental Microbiology 21(2): 682-701, 2019

Metaproteomic and metagenomic analyses of defined oceanic microbial populations using microwave cell fixation and flow cytometric sorting. Fems Microbiology Ecology 74(1): 10-18, 2010

An integrated metagenomic/metaproteomic investigation of microbiota in dajiang-meju, a traditional fermented soybean product in Northeast China. Food Research International 115: 414-424, 2019