title: Wavelet-based peak detection and a new charge inference procedure for MS/MS implemented in ProteoWizard's msConvert.
abstract: We report the implementation of high-quality signal processing algorithms into ProteoWizard, an efficient, open-source software package designed for analyzing proteomics tandem mass spectrometry data. Specifically, a new wavelet-based peak-picker (CantWaiT) and a precursor charge determination algorithm (Turbocharger) have been implemented. These additions into ProteoWizard provide universal tools that are independent of vendor platform for tandem mass spectrometry analyses and have particular utility for intralaboratory studies requiring the advantages of different platforms convergent on a particular workflow or for interlaboratory investigations spanning multiple platforms. We compared results from these tools to those obtained using vendor and commercial software, finding that in all cases our algorithms resulted in a comparable number of identified peptides for simple and complex samples measured on Waters, Agilent, and AB SCIEX quadrupole time-of-flight and Thermo Q-Exactive mass spectrometers. The mass accuracy of matched precursor ions also compared favorably with vendor and commercial tools. Additionally, typical analysis runtimes (∼1-100 ms per MS/MS spectrum) were short enough to enable the practical use of these high-quality signal processing tools for large clinical and research data sets.
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, Tennessee 37232-8340, United States.
authors.forename: William R
authors.initials: WR
authors.lastname: French
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Zimmerman
authors.forename: Birgit
authors.initials: B
authors.lastname: Schilling
authors.forename: Bradford W
authors.initials: BW
authors.lastname: Gibson
authors.forename: Christine A
authors.initials: CA
authors.lastname: Miller
authors.forename: R Reid
authors.initials: RR
authors.lastname: Townsend
authors.forename: Stacy D
authors.initials: SD
authors.lastname: Sherrod
authors.forename: Cody R
authors.initials: CR
authors.lastname: Goodwin
authors.forename: John A
authors.initials: JA
authors.lastname: McLean
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D010455:Peptides / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides
keywords: Continuous wavelet transformation; deisotoping; mass spectrometry; open-source software; peak-picking; precursor charge determination; signal deconvolution