Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis
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Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis. / Steigerwald, Sophia; Sinha, Ankit; Fort, Kyle L; Zeng, Wen-Feng; Niu, Lili; Wichmann, Christoph; Kreutzmann, Arne; Mourad, Daniel; Aizikov, Konstantin; Grinfeld, Dmitry; Makarov, Alexander; Mann, Matthias; Meier, Florian.
In: Molecular and Cellular Proteomics, 2024.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis
AU - Steigerwald, Sophia
AU - Sinha, Ankit
AU - Fort, Kyle L
AU - Zeng, Wen-Feng
AU - Niu, Lili
AU - Wichmann, Christoph
AU - Kreutzmann, Arne
AU - Mourad, Daniel
AU - Aizikov, Konstantin
AU - Grinfeld, Dmitry
AU - Makarov, Alexander
AU - Mann, Matthias
AU - Meier, Florian
N1 - Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.
PY - 2024
Y1 - 2024
N2 - Optimizing data-independent acquisition (DIA) methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here we describe a real-time, full mass range implementation of the Phase-constrained Spectrum Deconvolution Method (ΦSDM) for Orbitrap TM mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation (eFT) signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2-hour analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here the number of identified protein groups and peptides increased by >15% in comparison to eFT processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.
AB - Optimizing data-independent acquisition (DIA) methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here we describe a real-time, full mass range implementation of the Phase-constrained Spectrum Deconvolution Method (ΦSDM) for Orbitrap TM mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation (eFT) signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2-hour analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here the number of identified protein groups and peptides increased by >15% in comparison to eFT processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.
U2 - 10.1016/j.mcpro.2024.100713
DO - 10.1016/j.mcpro.2024.100713
M3 - Journal article
C2 - 38184013
JO - Molecular and Cellular Proteomics
JF - Molecular and Cellular Proteomics
SN - 1535-9476
M1 - 100713
ER -
ID: 379591317