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 -