title: Instant spectral assignment for advanced decision tree-driven mass spectrometry.
abstract: We have developed and implemented a sequence identification algorithm (inSeq) that processes tandem mass spectra in real-time using the mass spectrometer's (MS) onboard processors. The inSeq algorithm relies on accurate mass tandem MS data for swift spectral matching with high accuracy. The instant spectral processing technology takes ∼16 ms to execute and provides information to enable autonomous, real-time decision making by the MS system. Using inSeq and its advanced decision tree logic, we demonstrate (i) real-time prediction of peptide elution windows en masse (∼3 min width, 3,000 targets), (ii) significant improvement of quantitative precision and accuracy (~3x boost in detected protein differences), and (iii) boosted rates of posttranslation modification site localization (90% agreement in real-time vs. offline localization rate and an approximate 25% gain in localized sites). The decision tree logic enabled by inSeq promises to circumvent problems with the conventional data-dependent acquisition paradigm and provides a direct route to streamlined and expedient targeted protein analysis.
authors.affiliation: Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Bailey
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Rose
authors.forename: Graeme C
authors.initials: GC
authors.lastname: McAlister
authors.forename: Justin
authors.initials: J
authors.lastname: Brumbaugh
authors.forename: Pengzhi
authors.initials: P
authors.lastname: Yu
authors.forename: Craig D
authors.initials: CD
authors.lastname: Wenger
authors.forename: Michael S
authors.initials: MS
authors.lastname: Westphall
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D002478:Cells, Cultured; D002851:Chromatography, High Pressure Liquid; D030562:Databases, Protein; D003663:Decision Trees; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D015203:Reproducibility of Results; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*; D013997:Time Factors
chemical_list: D010455:Peptides; D011506:Proteins