title: msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry-Based Fragmentation in Metabolomics.
abstract: Tandem mass spectrometry (MS/MS or MS2) is a widely used approach for structural annotation and identification of metabolites in complex biological samples. The importance of assessing the contribution of the precursor ion within an isolation window for MS2experiments has been previously detailed in proteomics, where precursor ion purity influences the quality and accuracy of matching to mass spectral libraries, but to date, there has been little attention to this data-processing technique in metabolomics. Here, we present msPurity, a vendor-independent R package for liquid chromatography (LC) and direct infusion (DI) MS2that calculates a simple metric to describe the contribution of the selected precursor. The precursor purity metric is calculated as "intensity of a selected precursor divided by the summed intensity of the isolation window". The metric is interpolated at the recorded point of MS2acquisition using bordering full-scan spectra. Isotopic peaks of the selected precursor can be removed, and low abundance peaks that are believed to have limited contribution to the resulting MS2spectra are removed. Additionally, the isolation efficiency of the mass spectrometer can be taken into account. The package was applied to Data Dependent Acquisition (DDA)-based MS2metabolomics data sets derived from three metabolomics data repositories. For the 10 LC-MS2DDA data sets with > ±1 Da isolation windows, the median precursor purity score ranged from 0.67 to 0.96 (scale = 0 to +1). The R package was also used to assess precursor purity of theoretical isolation windows from LC-MS data sets of differing sample types. The theoretical isolation windows being the same width used for an anticipated DDA experiment (±0.5 Da). The most complex sample had a median precursor purity score of 0.46 for the 64,498 XCMS determined features, in comparison to the less spectrally complex sample that had a purity score of 0.66 for 5071 XCMS features. It has been previously reported in proteomics that a purity score of <0.5 can produce unreliable spectra matching results. With this assumption, we show that for complex samples there will be a large number of metabolites where traditional DDA approaches will struggle to provide reliable annotations or accurate matches to mass spectral libraries.
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Thomas N
authors.identifier: 0000-0002-5915-7980
authors.initials: TN
authors.lastname: Lawson
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Ralf J M
authors.initials: RJ
authors.lastname: Weber
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Martin R
authors.initials: MR
authors.lastname: Jones
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Andrew J
authors.identifier: 0000-0001-6648-6881
authors.initials: AJ
authors.lastname: Chetwynd
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Giovanny
authors.identifier: 0000-0002-7154-7244
authors.initials: G
authors.lastname: Rodrı Guez-Blanco
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Di Guida
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Viant
authors.affiliation: School of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental Sciences, University of Birmingham , Edgbaston, Birmingham, B15 2TT, United Kingdom.
authors.forename: Warwick B
authors.identifier: 0000-0001-6924-0027
authors.initials: WB
authors.lastname: Dunn
mesh_terms: D001331:Automation; D002851:Chromatography, High Pressure Liquid; D007477:Ions / Q000737:chemistry; D055432:Metabolomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D007477:Ions