Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis

• DOI: 10.1016/j.mcpro.2024.100713
• Publication Date: 2024-01-04T18:21:22Z
• Authors: Sophia Steigerwald; Ankit Sinha; Kyle L. Fort; Wen-Feng Zeng; Lili Niu; Christoph Wichmann; Arne Kreutzmann; Daniel Mourad; Konstantin Aizikov; Dmitry Grinfeld; Alexander Makarov; Matthias Mann; Florian Meier
• Keywords: Orbitrap; Proteome; Label-free Quantification

Optimizing data-independent acquisition (DIA) methods for proteomics applications often requires balancing spectral resolution and speed. Here we describe a real-time, full mass range implementation of the Phase-constrained Spectrum Deconvolution Method (ΦSDM) OrbitrapTM spectrometry that increases resolving power without increasing scan time. Comparing its performance to standard enhanced Fourier transformation (eFT) signal processing revealed increased ΦSDM is beneficial in areas high peptide density comes with greater ability resolve low-abundance signals. In 2-hour analysis 200 ng HeLa digest, this resulted an increase 16% number quantified peptides. As speed becomes even more important when using fast chromatographic gradients, further applied shorter gradient lengths (21, 12, 5 min). While improved identification rates quality all tested it proved particularly advantageous min gradient. identified protein groups peptides by >15% comparison eFT processing. conclusion, alternative algorithm Orbitrap data can improve benefit quantitative accuracy typical experiments, especially short gradients.