Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.

Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate protein catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration of mass spectrometry-based proteomics data with computational proteome predict...

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Main Authors:	Brandi L Cantarel, Alison R Erickson, Nathan C VerBerkmoes, Brian K Erickson, Patricia A Carey, Chongle Pan, Manesh Shah, Emmanuel F Mongodin, Janet K Jansson, Claire M Fraser-Liggett, Robert L Hettich
Format:	article
Language:	EN
Published:	Public Library of Science (PLoS) 2011
Subjects:	Medicine R Science Q
Online Access:	https://doaj.org/article/668b5a86f28b45b38231d8828db584f9
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spelling	oai:doaj.org-article:668b5a86f28b45b38231d8828db584f92021-11-18T07:33:41ZStrategies for metagenomic-guided whole-community proteomics of complex microbial environments.1932-620310.1371/journal.pone.0027173https://doaj.org/article/668b5a86f28b45b38231d8828db584f92011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22132090/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate protein catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration of mass spectrometry-based proteomics data with computational proteome predictions from environmental metagenomic sequences has been challenging because of the variable overlap between proteomic datasets and corresponding short-read nucleotide sequence data. In this study, we have benchmarked several strategies for increasing microbial peptide spectral matching in metaproteomic datasets using protein predictions generated from matched metagenomic sequences from the same human fecal samples. Additionally, we investigated the impact of mass spectrometry-based filters (high mass accuracy, delta correlation), and de novo peptide sequencing on the number and robustness of peptide-spectrum assignments in these complex datasets. In summary, we find that high mass accuracy peptide measurements searched against non-assembled reads from DNA sequencing of the same samples significantly increased identifiable proteins without sacrificing accuracy.Brandi L CantarelAlison R EricksonNathan C VerBerkmoesBrian K EricksonPatricia A CareyChongle PanManesh ShahEmmanuel F MongodinJanet K JanssonClaire M Fraser-LiggettRobert L HettichPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 11, p e27173 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Brandi L Cantarel Alison R Erickson Nathan C VerBerkmoes Brian K Erickson Patricia A Carey Chongle Pan Manesh Shah Emmanuel F Mongodin Janet K Jansson Claire M Fraser-Liggett Robert L Hettich Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
description	Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate protein catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration of mass spectrometry-based proteomics data with computational proteome predictions from environmental metagenomic sequences has been challenging because of the variable overlap between proteomic datasets and corresponding short-read nucleotide sequence data. In this study, we have benchmarked several strategies for increasing microbial peptide spectral matching in metaproteomic datasets using protein predictions generated from matched metagenomic sequences from the same human fecal samples. Additionally, we investigated the impact of mass spectrometry-based filters (high mass accuracy, delta correlation), and de novo peptide sequencing on the number and robustness of peptide-spectrum assignments in these complex datasets. In summary, we find that high mass accuracy peptide measurements searched against non-assembled reads from DNA sequencing of the same samples significantly increased identifiable proteins without sacrificing accuracy.
format	article
author	Brandi L Cantarel Alison R Erickson Nathan C VerBerkmoes Brian K Erickson Patricia A Carey Chongle Pan Manesh Shah Emmanuel F Mongodin Janet K Jansson Claire M Fraser-Liggett Robert L Hettich
author_facet	Brandi L Cantarel Alison R Erickson Nathan C VerBerkmoes Brian K Erickson Patricia A Carey Chongle Pan Manesh Shah Emmanuel F Mongodin Janet K Jansson Claire M Fraser-Liggett Robert L Hettich
author_sort	Brandi L Cantarel
title	Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
title_short	Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
title_full	Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
title_fullStr	Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
title_full_unstemmed	Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
title_sort	strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/668b5a86f28b45b38231d8828db584f9
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Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.

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