Instant spectral assignment for advanced decision tree-driven mass spectrometry.

Proceedings of the National Academy of Sciences of the United States of America
Derek J BaileyJoshua J Coon

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.

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Citations

Jul 21, 2012·Analytical Chemistry·Alexandre A ShvartsburgNeil L Kelleher
May 4, 2013·Analytical Chemistry·Christopher M RoseJoshua J Coon
Feb 27, 2013·Chemical Reviews·Yaoyang ZhangJohn R Yates
Jan 18, 2013·Journal of Proteome Research·Craig D Wenger, Joshua J Coon
Dec 5, 2012·Nature Reviews. Genetics·A F Maarten AltelaarAlbert J R Heck
Aug 7, 2012·Molecular & Cellular Proteomics : MCP·Amelia C PetersonJoshua J Coon
Jan 23, 2016·Mass Spectrometry Reviews·Luminita Moruz, Lukas Käll
Nov 6, 2015·Analytical Chemistry·Nicholas M Riley, Joshua J Coon
Nov 13, 2015·Analytical Chemistry·Janice MayneDaniel Figeys
Dec 20, 2015·Proteomics·Andreas HentschelRobert Ahrends
Mar 5, 2013·Proteomics·James T WebberJarrod A Marto
Jul 1, 2015·Journal of the American Society for Mass Spectrometry·Bin Ma
Jun 27, 2015·Journal of the American Society for Mass Spectrometry·Christopher M RoseJoshua J Coon
Jul 10, 2013·Current Opinion in Chemical Biology·Anna E Merrill, Joshua J Coon
Jul 1, 2015·Journal of the American Society for Mass Spectrometry·Scott A Robotham, Jennifer S Brodbelt
Jul 16, 2016·The Analyst·Irina A TarasovaMikhail V Gorshkov
Mar 11, 2015·Molecular & Cellular Proteomics : MCP·Sebastien GallienBruno Domon
Dec 12, 2018·BioMed Research International·Zichuan FanYalan Dai
Dec 1, 2014·Clinical and Translational Medicine·Maneesh BhargavaDavid H Ingbar
Jul 30, 2021·Expert Review of Proteomics·Jennie R LillMarkus Schirle
Apr 7, 2020·Analytical Chemistry·Qing YuDevin K Schweppe
Mar 13, 2014·Journal of Proteome Research·Derek J BaileyJoshua J Coon
Aug 21, 2021·Molecular & Cellular Proteomics : MCP·Florian MeierMatthias Mann
Jul 13, 2019·Analytical Chemistry·Paul D HutchinsJoshua J Coon
Dec 7, 2018·Journal of Proteome Research·Christopher M RoseDonald S Kirkpatrick

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