title: Autopiquer - a Robust and Reliable Peak Detection Algorithm for Mass Spectrometry.
abstract: We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time-consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data, whilst keeping as much of the (isotopic) structure as possible. This algorithm has been successfully demonstrated for both peak detection and spectral compression on data from many different classes of mass spectrometer and for different sample types, and this approach should also be extendible to other types of data that contain regularly spaced discrete peaks. Graphical Abstract ᅟ.
authors.affiliation: Department of Chemistry and Forensics, Nottingham Trent University, Nottingham, NG11 8NS, UK. david.kilgour@ntu.ac.uk.
authors.forename: David P A
authors.initials: DPA
authors.lastname: Kilgour
authors.affiliation: EastCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
authors.forename: Sam
authors.initials: S
authors.lastname: Hughes
authors.affiliation: Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, 21201, USA.
authors.forename: Samantha L
authors.initials: SL
authors.lastname: Kilgour
authors.affiliation: EastCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
authors.forename: C Logan
authors.initials: CL
authors.lastname: Mackay
authors.affiliation: Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
authors.forename: Magnus
authors.initials: M
authors.lastname: Palmblad
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA.
authors.forename: Bao Quoc
authors.initials: BQ
authors.lastname: Tran
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA.
authors.forename: Young Ah
authors.initials: YA
authors.lastname: Goo
authors.affiliation: Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, 21201, USA.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Ernst
authors.affiliation: EastCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Clarke
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
keywords: Mass spectrometry; Peak detection; Threshold