Protocol abstract
Nature Protocols 3, - 471 - 485 (2008)
Published online: 28 February 2008 | doi:10.1038/nprot.2007.512
Subject Categories: Computational and theoretical biology | Isolation, purification and separation | Spectroscopy and structural analysis
Explanatory signal interpretation and metabolite identification strategies for nominal mass FIE-MS metabolite fingerprints
David P Overy1,3, David P Enot1, Kathleen Tailliart1, Helen Jenkins2, David Parker1, Manfred Beckmann1 & John Draper1
Abstract
Flow injection electrospray mass spectrometry (FIE-MS) metabolite fingerprinting is widely used as a 'first pass' screen for compositional differences, where discrimination between samples can be achieved without any preconceptions. Powerful data analysis algorithms can be used to select and rank FIE-MS fingerprint variables highly explanatory of the biological problem under investigation. We describe how to create a species-specific FIE-MS/MSn metabolite database and how to then query the database to predict the identity of highly significant variables within FIE-MS fingerprints. The protocol details how to interpret m/z signals within the explanatory variable list based on a correlation analysis in conjunction with an investigation of mathematical relationships regarding (de)protonated molecular ions, salt adducts, neutral losses and dimeric associations routinely observed in FIE-MS fingerprints. Although designed for use by biologists/analytical chemists, collaboration with data-mining experts is generally advised. The protocol is applicable in any areas of bioscience research involving FIE-MS fingerprinting.
- Institute of Biological Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK, SY23 3DA.
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, UK, SY23 3DB.
- Present address: CIBE, Merck Sharp & Dohme de España, Madrid 28027, Spain.
Correspondence to: John Draper1 e-mail: jhd@aber.ac.uk