Maria A. van Agthoven

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. Phase-corrected absorption mode data processing on limited data sets has previously shown improvements in signal-to-noise ratio (SNR) and resolving power by a factor of 2. Here, we have expanded phase-corrected absorption mode data processing to 2D mass spectra regardless of size and frequency range. We have applied phase-corrected 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 phase-corrected absorption mode data processing significantly improves both the SNR 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.

Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that does not rely on ion isolation to correlate the precursor and fragment ions. On a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), 2D MS instead uses the modulation of precursor ion radii inside the ICR cell before fragmentation and yields 2D mass spectra that show the fragmentation patterns of all the analytes. In this study, we perform 2D MS for the first time with quadrupolar detection in a dynamically harmonized ICR cell. We discuss the advantages of quadrupolar detection in 2D MS and how we adapted existing data processing techniques for accurate frequency-to-mass conversion. We apply 2D MS with quadrupolar detection to the top-down analysis of covalently labeled ubiquitin with ECD fragmentation, and we develop a workflow for label-free relative quantification of biomolecule isoforms in 2D MS.

Due to the natural dispersity that is present in synthetic polymers, an added complexity is always present in the analysis of polymeric species. Tandem mass spectrometry analysis requires the isolation of individual precursors before a fragmentation event to allow the unambiguous characterization of these species and is not viable at certain levels of complexity due to achievable isolation widths. Two-dimensional mass spectrometry (2DMS) fragments ions and correlates fragments with their corresponding precursors without the need for isolation. In this study, 2DMS electron capture dissociation (ECD) fragmentation of a polyoxazoline and polyacrylamide species was carried out, resulting in the analysis of byproducts and individual polymer species without the use of chromatographic techniques. This study shows that 2DMS ECD is a powerful tool for the analysis of polyacrylamide and polyoxazoline species and offers a new dimension in the characterization of polymers.

Two-dimensional mass spectrometry (2D MS) on an FT-ICR mass analyzer allows for tandem mass spectrometry without requiring ion isolation. In the ICR cell, precursor ion radii are modulated before fragmentation, which results in modulation of the abundance of their fragments. The resulting 2D mass spectrum enables correlation between precursor and fragment ions. In standard broadband 2D MS, the range of precursor ion cyclotron frequencies is determined by the lowest mass-to-charge (m/z) ratio to be fragmented in the 2D MS experiment, which leads to precursor ion m/z ranges that are much wider than necessary, thereby limiting the resolving power for precursor ions and the accuracy of the correlation between precursor and fragment ions. We present narrowband modulation 2D MS, which increases the precursor ion resolving power by reduc-ing the precursor ion m/z range, with the aim of resolving the fragment ion patterns of overlapping isotopic distributions. In this proof-of-concept study, we compare broadband and narrowband modulation 2D mass spectra of an equimolar mixture of histone peptide isoforms. In narrowband modulation 2D MS, we were able to separate the fragment ion patterns of all 13C isotopes of the different histone peptide forms. We further demonstrate the potential of narrowband 2D MS for label-free quantification of peptides.

Fourier transform ion cyclotron resonance mass analysers (FT-ICR MS) can offer the highest resolutions and mass accuracies in mass spectrometry. Mass spectra acquired in an FT-ICR MS can yield accurate elemental compositions of all compounds in a complex sample. Fragmentation caused by ion–neutral, ion–electron, or ion–photon interactions leads to more detailed structural information on compounds. The most often used method to correlate compounds and their fragment ions is to isolate the precursor ions from the sample before fragmentation. Two-dimensional mass spectrometry (2D MS) offers a method to correlate precursor and fragment ions without requiring precursor isolation. 2D MS therefore enables easy access to the fragmentation patterns of all compounds from complex samples. In this article, the principles of FT-ICR MS are reviewed and the 2D MS experiment is explained. Data processing for 2D MS is detailed, and the interpretation of 2D mass spectra is described.

A Smart Numerical Annotation Procedure (SNAP) allows automated MS identification of proteins modified by metals and other elements in dense LCMS and LC-MS/MS data sets, including those for metallodrug targets and natural metalloproteins.

Rationale: Two‐dimensional mass spectrometry (2D MS) is a technique that correlates precursor and product ions in a sample without requiring prior ion isolation. Until now, this technique has only been implemented on Fourier transform ion cyclotron resonance mass spectrometers. By coupling 2D MS techniques in linear ion traps (LITs) with a mass analyser with a fast duty cycle (e.g. time‐of‐flight), data‐independent tandem mass spectrometry techniques can be compatible on a liquid chromatography (LC) or gas chromatography (GC) timescale. Methods: The feasibility of 2D MS in a LIT is explored using SIMION ion trajectory calculations. Results: By applying stored waveform inverse Fourier transform techniques for radial excitation on a LIT, the sizes of ion clouds were found to be modulated according to the ions' resonant frequencies in the LIT. By simulating a laser‐based fragmentation at the centre of the LIT after the radius modulation step, product ion abundances were found to be modulated according to the resonant frequency of their precursor. Conclusions: A 2D mass spectrum could be obtained using the results from the simulation. This in silico model shows the feasibility of 2D MS on a LIT. 2D MS in a LIT allows for tandem mass spectrometry without ion isolation. Copyright © 2017 John Wiley & Sons, Ltd.

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their pr...