Fellgett Revisited: On the Nature of Noise in Two-Dimensional Mass Spectrometry

Two-dimensional mass spectrometry (2DMS) is a truly data-independent acquisition technique used in the analysis of complex mixtures; however, the nature of the noise within these spectra is not well understood. In this work, 2DMS is tested for conformity with the Fellgett principle: (signal/noise) ∝ √ (no. of data points). Since 2DMS functions through the modulation of ions through a fragmentation region across many scans, the individual scans are considered data points in this experiment. Random noise was shown to be prevalent as the main source of noise in this experiment with minor systematic noise. This means that the minimum size for a 2DMS spectrum that displays a target fragment ion can be determined using a fast-2D equation detailed herein. The effects of existing denoising algorithms were also found to change the relationship between the signal-to-noise ratio and the scan numbers to be of a quasi-linear nature rather than the square root trend observed before denoising.

Molecular analysis of the extracellular microenvironment: from form to function

The extracellular matrix (ECM) proteome represents an important component of the tissue microenvironment that controls chemical flux and induces cell signaling through encoded structure. The analysis of the ECM represents an analytical challenge through high levels of post-translational modifications, protease-resistant structures, and crosslinked, insoluble proteins. This review provides a comprehensive overview of the analytical challenges involved in addressing the complexities of spatially profiling the extracellular matrix proteome. A synopsis of the process of synthesizing the ECM structure, detailing inherent chemical complexity, is included to present the scope of the analytical challenge. Current chromatographic and spatial techniques addressing these challenges are detailed. Capabilities for multimodal multiplexing with cellular populations are discussed with a perspective on developing a holistic view of disease processes that includes both the cellular and extracellular microenvironment.

Spectral Features Differentiate Aging-Induced Changes in Parchment-A Combined Approach of UV/VIS, µ-ATR/FTIR and µ-Raman Spectroscopy with Multivariate Data Analysis

From the moment of production, artworks are constantly exposed to changing environmental factors potentially inducing degradation. Therefore, detailed knowledge of natural degradation phenomena is essential for proper damage assessment and preservation. With special focus on written cultural heritage, we present a study on the degradation of sheep parchment employing accelerated aging with light (295-3000 nm) for one month, 30/50/80% relative humidity (RH) and 50 ppm sulfur dioxide with 30/50/80%RH for one week. UV/VIS spectroscopy detected changes in the sample surface appearance, showing browning after light-aging and increased brightness after SO₂-aging. Band deconvolution of ATR/FTIR and Raman spectra and factor analysis of mixed data (FAMD) revealed characteristic changes of the main parchment components. Spectral features for degradation-induced structural changes of collagen and lipids turned out to be different for the employed aging parameters. All aging conditions induced denaturation (of different degrees) indicated by changes in the secondary structure of collagen. Light treatment resulted in the most pronounced changes for collagen fibrils in addition to backbone cleavage and side chain oxidations. Additional increased disorder for lipids was observed. Despite shorter exposure times, SO₂-aging led to a weakening of protein structures induced by transitions of stabilizing disulfide bonds and side chain oxidations.

Ultra-Accurate Correlation between Precursor and Fragment Ions in Two-Dimensional Mass Spectrometry: Acetylated vs Trimethylated Histone Peptides

Two-dimensional mass spectrometry (2D MS) is a method for tandem mass spectrometry in which precursor and fragment ions are correlated by manipulating ion radii rather than by ion isolation. A 2D mass spectrum contains the fragmentation patterns of all analytes in a sample, acquired in parallel. We report ultrahigh-resolution narrowband 2D mass spectra of a mixture of two histone peptides with the same sequence, one of which carries an acetylation and the other a trimethylation (m/z 0.006 difference). We reduced the distance between data points in the precursor ion dimension and compared the accuracy of the precursor-fragment correlation with the resolving power. We manage to perform label-free quantification on the histone peptide mixture and show that precursor and fragment ions can be accurately correlated even though the precursor ions are not resolved. Finally, we show that increasing the resolution of a 2D mass spectrum in the precursor ion dimension too far can lead to a decline in the signal-to-noise ratio.

In Silico Demonstration of Two-Dimensional Mass Spectrometry Using Spatially Dependent Fragmentation

Two-dimensional mass spectrometry (2DMS) allows for the analysis of complex mixtures of all kinds at high speed and resolution without data loss from isolation or biased acquisition, effectively generating tandem mass spectrometry information for all ions at once. Currently, this technique is limited to instruments utilizing an ion trap such as the Fourier transform ion cyclotron resonance or linear ion traps. To overcome this limitation, new fragmentation waveforms were used in either a temporal or spatial configuration, allowing for the application of 2DMS on a much wider array of instruments. A simulated example of a time-of-flight-based instrument is shown with the new waveforms, which allowed for the correlation of fragment ions to their respective precursors through the processing of the modulation of fragmentation intensity with a Fourier transform. This application indicated that 2D modulation and Fourier precursor/fragment intensity correlation are possible in any case where separation, either temporally or spatially, can be achieved, allowing 2DMS to be applied to almost every type of mass spectrometry instrument.

Characterization Across a Dispersity: Polymer Mass Spectrometry in the Second Dimension

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.

Narrowband Modulation Two-Dimensional Mass Spectrometry and Label-Free Relative Quantification of Histone Peptides

Two-dimensional mass spectrometry (2D MS) on a Fourier transform ion cyclotron resonance (FT-ICR) mass analyzer allows for tandem mass spectrometry without requiring ion isolation. In the ICR cell, the precursor ion radii are modulated before fragmentation, which results in modulation of the abundance of their fragments. The resulting 2D mass spectrum enables a correlation between the precursor and fragment ions. In a 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 the precursor and fragment ions. We present narrowband modulation 2D MS, which increases the precursor ion resolving power by reducing 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.

Metallocomplex-Peptide Interactions Studied by Ultrahigh Resolution Mass Spectrometry

The Os^II arene anticancer complex [(η⁶-bip)Os(en)Cl]⁺ (Os1-Cl; where bip = biphenyl and en = ethylenediamine) binds strongly to DNA¹ and biomolecules. Here we investigate the interaction between Os1-Cl and the model protein, BSA, using ultrahigh resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The specific binding location of Os1 on BSA was investigated with the use of collisionally activated dissociation (CAD) and electron capture dissociation (ECD). CAD MS/MS was found to dissociate the osmium complex from the metallo-peptide complex readily producing unmodified fragments and losing location information. ECD MS/MS, however, successfully retains the osmium modification on the peptides upon fragmentation allowing localization of metallocomplex binding. This study reveals that lysine is a possible binding location for Os1-Cl, apart from the expected binding sites at methionine, histidine, and cysteine. Using a nano liquid chromatography (nLC)-FT-ICR ECD MS/MS study, multiple binding locations, including the N-terminus and C-terminus of digested peptides, glutamic acid, and lysine were also revealed. These results show the multitargeting binding ability of the organo-osmium compound and can be used as a standard workflow for more complex systems, e.g., metallocomplex-cell MS analysis, to evaluate their behavior toward commonly encountered biomolecules.

Phase relationships in two-dimensional mass spectrometry

Two-dimensional mass spectrometry (2D MS) is a data-independent tandem mass spectrometry technique in which precursor and fragment ion species can be correlated without the need for prior ion isolation. The behavior of phase in 2D Fourier transform mass spectrometry is investigated with respect to the calculation of phase-corrected absorption-mode 2D mass spectra. 2D MS datasets have a phase that is defined differently in each dimension. In both dimensions, the phase behavior of precursor and fragment ions is found to be different. The dependence of the phase for both precursor and fragment ion signals on various parameters (e.g., modulation frequency, shape of the fragmentation zone) is discussed. Experimental data confirms the theoretical calculations of the phase in each dimension. Understanding the phase relationships in a 2D mass spectrum is beneficial to the development of possible algorithms for phase correction, which may improve both the signal-to-noise ratio and the resolving power of peaks in 2D mass spectra.

Two-dimensional mass spectrometry: new perspectives for tandem mass spectrometry

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.

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

Can Two-Dimensional IR-ECD Mass Spectrometry Improve Peptide de Novo Sequencing?

Two-dimensional mass spectrometry (2D MS) correlates precursor and fragment ions without ion isolation in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) for tandem mass spectrometry. Infrared activated electron capture dissociation (IR-ECD), using a hollow cathode configuration, generally yields more information for peptide sequencing in tandem mass spectrometry than ECD (electron capture dissociation) alone. The effects of the fragmentation zone on the 2D mass spectrum are investigated as well as the structural information that can be derived from it. The enhanced structural information gathered from the 2D mass spectrum is discussed in terms of how de novo peptide sequencing can be performed with increased confidence. 2D IR-ECD MS is shown to sequence peptides, to distinguish between leucine and isoleucine residues through the production of w ions as well as between C-terminal ( b/ c) and N-terminal ( y/ z) fragments through the use of higher harmonics, and to assign and locate peptide modifications.

Bottom-Up Two-Dimensional Electron-Capture Dissociation Mass Spectrometry of Calmodulin

Two-dimensional mass spectrometry (2D MS) is a tandem mass spectrometry technique that allows data-independent fragmentation of all precursors in a mixture without previous isolation, through modulation of the ion cyclotron frequency in the ICR-cell prior to fragmentation. Its power as an analytical technique has been proven particularly for proteomics. Recently, a comparison study between 1D and 2D MS has been performed using infrared multiphoton dissociation (IRMPD) on calmodulin (CaM), highlighting the capabilities of the technique in both top-down (TDP) and bottom-up proteomics (BUP). The goal of this work is to expand this study on CaM using electron-capture dissociation (ECD) 2D MS as a single complementary BUP experiment in order to enhance the cleavage coverage of the protein under analysis. By adding the results of the BUP 2D ECD MS to the 2D IRMPD MS analysis of CaM, the total cleavage coverage increased from ~40% to ~68%. Graphical abstract ᅟ.

Nonuniform Sampling Acquisition of Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Increased Mass Resolution of Tandem Mass Spectrometry Precursor Ions

Obtaining the full MS/MS map for fragments and precursors of complex mixtures without hyphenation with chromatographic separation by a data-independent acquisition is a challenge in mass spectrometry which is solved by two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). Until now 2D FTICR MS afforded only a moderate resolution for precursor ion since this resolution is limited by the number of evolution interval steps to which the number of scans, the acquisition time, and the sample consumption are proportional. An overnight acquisition is already required to reach a quadrupole mass filter-like unit mass resolution. Here, we report that 2D FTICR MS using nonuniform sampling (NUS) obtained by randomly skipping points in the first dimension corresponding to the precursor selection gives access, after data processing, to the same structural information contained in a complex mixture. The resolution increases roughly as the inverse of the NUS ratio, up to 26 times at NUS 1/32, leading to an acquisition time reduced in the same ratio compared to a classical acquisition at the same resolution. As an example, the analysis of a natural oil is presented.

Two-dimensional mass spectrometry in a linear ion trap, an in silico model

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 Mass Spectrometry for Proteomics, a Comparative Study with Cytochrome c

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows the correlation between precursor and fragment ions in tandem mass spectrometry without the need to isolate the precursor ion beforehand. 2D FT-ICR MS has been optimized as a data-independent method for the structural analysis of compounds in complex samples. Data processing methods and denoising algorithms have been developed to use it as an analytical tool. In the present study, the capabilities of 2D FT-ICR MS are explored with a tryptic digest of cytochrome c with both ECD and IRMPD as fragmentation modes. The 2D mass spectra showed useful fragmentation patterns of peptides over a dynamic range of almost 400. By using a quadratic calibration, fragment ion peaks could be successfully assigned. The correlation between precursor and fragment ions in the 2D mass spectra was more accurate than in MS/MS spectra after quadrupole isolation, due to the limitations of quadrupole isolation. The use of the second dimension allowed for successful fragment assignment from precursors that were separated by only m/z 0.0156. The resulting cleavage coverage of cytochrome c almost matched data provided by high-resolution FT-ICR MS/MS analysis, but the 2D FT-ICR MS method required only one experimental scan.