Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data View Full Text


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Article Info

DATE

2011-03-05

AUTHORS

Ying S. Ting, Scott A. Shaffer, Jace W. Jones, Wailap V. Ng, Robert K. Ernst, David R. Goodlett

ABSTRACT

Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MSn) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080–1092, 2007). Annotation of these MSn spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MSn spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MSn data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MSn spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MSn spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species. More... »

PAGES

856-866

References to SciGraph publications

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s13361-010-0055-y

    DOI

    http://dx.doi.org/10.1007/s13361-010-0055-y

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1027420390

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21472520


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