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Title: Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Subsurface Biogeochemical Research (SBR)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1154575
Resource Type:
Journal Article
Resource Relation:
Journal Name: Applied and Environmental Microbiology; Journal Volume: 72; Journal Issue: 3
Country of Publication:
United States
Language:
English

Citation Formats

D.,van der Lelie, C.,Lesaulnier, S.,McCorkle, J.,Geets, S.,Taghavi, and J.,Dunn. Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys. United States: N. p., 2006. Web. doi:10.1128/AEM.72.3.2092-2101.2006.
D.,van der Lelie, C.,Lesaulnier, S.,McCorkle, J.,Geets, S.,Taghavi, & J.,Dunn. Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys. United States. doi:10.1128/AEM.72.3.2092-2101.2006.
D.,van der Lelie, C.,Lesaulnier, S.,McCorkle, J.,Geets, S.,Taghavi, and J.,Dunn. Fri . "Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys". United States. doi:10.1128/AEM.72.3.2092-2101.2006.
@article{osti_1154575,
title = {Use of Single-Point Genome Signature Tags as a Universal Tagging Method for Microbial Genome Surveys},
author = {D.,van der Lelie and C.,Lesaulnier and S.,McCorkle and J.,Geets and S.,Taghavi and J.,Dunn},
abstractNote = {},
doi = {10.1128/AEM.72.3.2092-2101.2006},
journal = {Applied and Environmental Microbiology},
number = 3,
volume = 72,
place = {United States},
year = {Fri Mar 03 00:00:00 EST 2006},
month = {Fri Mar 03 00:00:00 EST 2006}
}
  • We describe and demonstrate a global strategy that extends the sensitivity, dynamic range, comprehensiveness, and throughput of proteomic measurements based upon the use of peptide accurate mass tags (AMTs) produced by global protein enzymatic digestion. The two-stage strategy exploits Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry to validate peptide AMTs for a specific organism, tissue or cell type from potential mass tags identified using conventional tandem mass spectrometry (MS/MS) methods, providing greater confidence in identifications as well as the basis for subsequent measurements without the need for MS/MS, and thus with greater sensitivity and increased throughput. A single high resolutionmore » capillary liquid chromatography separation combined with high sensitivity, high resolution and ac-curate FT-ICR measurements has been shown capable of characterizing peptide mixtures of significantly more than 10 5 components with mass accuracies of -1 ppm, sufficient for broad protein identification using AMTs. Other attractions of the approach include the broad and relatively unbiased proteome coverage, the capability for exploiting stable isotope labeling methods to realize high precision for relative protein abundance measurements, and the projected potential for study of mammalian proteomes when combined with additional sample fractionation. Using this strategy, in our first application we have been able to identify AMTs for 60% of the potentially expressed proteins in the organism Deinococcus radiodurans.« less
  • The genetic diversity across natural populations of the model organism, Populus, is extensive, containing a single nucleotide polymorphism roughly every 200 base pairs. When deviations from the reference genome occur in coding regions, they can impact protein sequences. Rather than relying on a static reference database to profile protein expression, we employed a peptide sequence tagging (PST) approach capable of decoding the plasticity of the Populus proteome. Using shotgun proteomics data from two genotypes of P. trichocarpa, a tag-based approach enabled the detection of 6,653 unexpected sequence variants. Through manual validation, our study investigated how the most abundant chemical modificationmore » (methionine oxidation) could masquerade as a sequence variant (AlaSer) when few site-determining ions existed. In fact, precise localization of an oxidation site for peptides with more than one potential placement was indeterminate for 70% of the MS/MS spectra. We demonstrate that additional fragment ions made available by high energy collisional dissociation enhances the robustness of the peptide sequence tagging approach (81% of oxidation events could be exclusively localized to a methionine). We are confident that augmenting fragmentation processes for a PST approach will further improve the identification of single amino acid polymorphism in Populus and potentially other species as well.« less
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