Absorption mode broadband 2D MS for proteomics and metabolomics

TL;DR

This paper extends absorption mode data processing to broadband 2D mass spectrometry, significantly enhancing signal-to-noise ratio and resolution in proteomics and metabolomics applications, enabling more accurate analysis of complex biological samples.

Contribution

It introduces a method for applying absorption mode processing to large 2D MS datasets, improving data quality and analysis accuracy in proteomics and metabolomics.

Findings

Improved signal-to-noise ratio by a factor of 2

Enhanced resolving power in 2D mass spectra

Increased sequence coverage and precursor-fragment correlation accuracy

Abstract

Two-dimensional mass spectrometry (2D MS) is a method for tandem mass spectrometry that enables the correlation between precursor and fragment ions without the need for ion isolation. On a Fourier transform ion cyclotron resonance mass spectrometer, the phase correction functions for absorption mode data processing were found to be linear in the precursor ion dimension and quadratic in the fragment ion dimension. Absorption mode data processing on limited data sets has previously shown improvements in signal-to-noise ratio and resolving power by a factor of 2. Here, we have expanded absorption mode data processing to 2D mass spectra regardless of size and frequency range. We have applied absorption mode 2D MS to top-down analysis of variously oxidized ubiquitin proteoforms generated by fast photochemical oxidation of proteins (FPOP) and to an extract of ergot alkaloids. We show that absorption mode data processing significantly improves both the signal-to-noise ratio and the resolving power of the 2D mass spectrum compared to standard magnitude mode in terms of sequence coverage in top-down proteomics, as well as the accuracy of precursor-fragment correlation in metabolomics.