High Dynamic Range Proteome Analysis with BoxCar DIA ......100 samples/day method on an Evosep One...

High dynamic range proteome analysis with BoxCar DIA and super-resolution Orbitrap mass spectrometry Florian Meier 1 , Kyle Fort 2 , Arne Kreutzmann 2 , Daniel Mourad 2 , Konstantin Aizikov 2 , Dmitry Grinfeld 2 , Johannes B Mueller 1 , André C Michaelis 1 , Alexander A. Makarov 2 and Matthias Mann 1, 3 1 Max Planck Institute of Biochemistry, Martinsried, Germany; 2 Thermo Fisher Scientific (GmbH) Bremen, Germany; 3 NNF Center for Protein Research University of Copenhagen, Copenhagen, Denmark ABSTRACT Purpose: Proteomics with BoxCar and data independent acquisition (DIA). Methods: Real-time ΦSDM (Phase-Constrained Spectrum Deconvolution Method) processing of full range mass spectra Results: Two-fold scan speed allows rapid proteome analysis and efficient implementation of BoxCar DIA. INTRODUCTION Phase-Constrained Spectrum Deconvolution Method (ΦSDM) [1] is a signal processing approach that uses the phase information in Orbitrap™ mass analyzers to improve resolution on a refined frequency grid. It translates into increased mass resolution without penalizing acquisition time. Due to its high computational cost, it has so far only been applied for offline calculations or in narrow m/z regions of interest [2]. MATERIALS AND METHODS Sample Preparation Whole-cell lysates and human blood samples were digested with trypsin/LysC and analyzed in single runs. Test Method(s) Four full range mass spectra were processed in parallel with a CUDA C++ implementation of the ΦSDM algorithm on an auxiliary computer equipped with Nvidia TITAN X GPU cards. Data Analysis All data were analyzed with Spectronaut™ software (Biognosys). RESULTS CONCLUSIONS Super-resolution Orbitrap mass spectrometry has a great potential for proteomics research with its increasing demand for high-throughput technologies. REFERENCES & ACKNOWLEDGEMENTS [1] D. Grinfeld et al., Anal. Chem., 89 (2), 1202–1211, 2017. [2] C. D. Kelstrup et al., J. Proteome Res., 17 (11), 4008–4016, 2018. [3] F. Meier et al., Nat. Methods, 15, 440-448, 2018. This research is partially supported by the European Union's Horizon 2020 research and innovation program under grant agreement 686547 (MSmed project). We thank O. Bernhardt, T. Gandhi and L. Reiter from Biognosys AG for software developments and access to Spectronaut. We further acknowledge L. Niu and P. Geyer for help with plasma samples. TRADEMARKS/LICENSING © 2020 Thermo Fisher Scientific Inc. All rights reserved. Spectronaut is a trademark of Biognosys AG. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries. This information is not intended to encourage use of these products in any manner that might infringe the intellectual property rights of others. Figure 1. Real-time Full MS spectra of charge state 12+ of ubiquitin with A, B enhanced Fourier Transformation (eFT, 32 ms and 64 ms transients) and C ΦSDM (32 ms transient) signal processing. Figure 2. Comparison of eFT and ΦSDM signal processing for DIA of a HeLa proteome digest with fast cycle times (A, B). Triplicates with the 100 samples/day method on an Evosep One LC coupled to a Thermo Scientific™ Orbitrap Exploris™ MS 480 with FAIMS (CV -45 V) (C). Figure 3. Rapid DIA analysis of human blood samples (30 samples/day). A, Dynamic range coverage in human plasma. B, Proteins quantified in five whole blood samples with BoxCar [3] DIA using eFT or ΦSDM signal processing. m/z 714.74 714.92 714.47 715.30 714.64 714.81 714.89 714.56 714.97 714.39 715.14 715.40 714.5 715.0 715.5 714.64 714.81 714.56 714.89 714.47 714.98 714.39 715.06 715.23 714.31 A eFT @32 ms B eFT @64 ms C ΦSDM @32 ms m/z m/z

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Transcript of High Dynamic Range Proteome Analysis with BoxCar DIA ......100 samples/day method on an Evosep One...

Page 1: High Dynamic Range Proteome Analysis with BoxCar DIA ......100 samples/day method on an Evosep One LC coupled to a Thermo Scientific Orbitrap Exploris MS480 with FAIMS(CV -45 V) (C).

1Max Planck Institute of Biochemistry, Martinsried, Germany; 2Thermo Fisher Scientific (GmbH) Bremen, Germany; 3NNF Center for Protein Research University of Copenhagen, Copenhagen, Denmark

ABSTRACT Purpose: Proteomics with BoxCar and data independentacquisition (DIA).Methods: Real-time ΦSDM (Phase-Constrained SpectrumDeconvolution Method) processing of full range mass spectraResults: Two-fold scan speed allows rapid proteome analysisand efficient implementation of BoxCar DIA.

INTRODUCTIONPhase-Constrained Spectrum Deconvolution Method (ΦSDM) [1]is a signal processing approach that uses the phase informationin Orbitrap™ mass analyzers to improve resolution on a refinedfrequency grid. It translates into increased mass resolutionwithout penalizing acquisition time. Due to its high computationalcost, it has so far only been applied for offline calculations or innarrow m/z regions of interest [2].

MATERIALS AND METHODSSample PreparationWhole-cell lysates and human blood samples were digested withtrypsin/LysC and analyzed in single runs.Test Method(s)Four full range mass spectra were processed in parallel with aCUDA C++ implementation of the ΦSDM algorithm on anauxiliary computer equipped with Nvidia TITAN X GPU cards.Data AnalysisAll data were analyzed with Spectronaut™ software (Biognosys).

RESULTS

CONCLUSIONSSuper-resolution Orbitrap mass spectrometry has a greatpotential for proteomics research with its increasing demandfor high-throughput technologies.

REFERENCES & ACKNOWLEDGEMENTS[1] D. Grinfeld et al., Anal. Chem., 89 (2), 1202–1211, 2017.[2] C. D. Kelstrup et al., J. Proteome Res., 17 (11), 4008–4016, 2018.[3] F. Meier et al., Nat. Methods, 15, 440-448, 2018.This research is partially supported by the European Union's Horizon 2020 researchand innovation program under grant agreement 686547 (MSmed project). We thankO. Bernhardt, T. Gandhi and L. Reiter from Biognosys AG for softwaredevelopments and access to Spectronaut. We further acknowledge L. Niu and P.Geyer for help with plasma samples.

TRADEMARKS/LICENSING© 2020 Thermo Fisher Scientific Inc. All rights reserved. Spectronaut is a trademarkof Biognosys AG. All other trademarks are the property of Thermo Fisher Scientificand its subsidiaries. This information is not intended to encourage use of theseproducts in any manner that might infringe the intellectual property rights of others.

Figure 1. Real-time Full MS spectra of charge state 12+ of ubiquitinwith A, B enhanced Fourier Transformation (eFT, 32 ms and 64 mstransients) and C ΦSDM (32 ms transient) signal processing.

Figure 2. Comparison of eFT and ΦSDM signal processing for DIA of aHeLa proteome digest with fast cycle times (A, B). Triplicates with the100 samples/day method on an Evosep One LC coupled to a ThermoScientific™ Orbitrap Exploris™ MS 480 with FAIMS (CV -45 V) (C).

Figure 3. Rapid DIA analysis of human blood samples (30samples/day). A, Dynamic range coverage in human plasma. B,Proteins quantified in five whole blood samples with BoxCar [3] DIAusing eFT or ΦSDM signal processing.

m/z

714.74

714.92714.47715.30

714.64714.81

714.89714.56714.97

714.39 715.14715.40

714.5 715.0 715.5

714.64714.81714.56714.89714.47

714.98714.39 715.06

715.23714.31

ΦSDM

A eFT @32 ms