A review of electron-capture and electron-transfer dissociation tandem mass spectrometry in polymer chemistry

Mass spectrometry imaging of N-linked glycans: Fundamentals and recent advances

With implications in several medical conditions, N-linked glycosylation is one of the most important posttranslation modifications present in all living organisms. Due to their nontemplate synthesis, glycan structures are extraordinarily complex and require multiple analytical techniques for complete structural elucidation. Mass spectrometry is the most common way to investigate N-linked glycans; however, with techniques such as liquid-chromatography mass spectrometry, there is complete loss of spatial information. Mass spectrometry imaging is a transformative analytical technique that can visualize the spatial distribution of ions within a biological sample and has been shown to be a powerful tool to investigate N-linked glycosylation. This review covers the fundamentals of mass spectrometry imaging and N-linked glycosylation and highlights important findings of recent key studies aimed at expanding and improving the glycomics imaging field.

Computational approaches to identify sites of phosphorylation

Due to their oftentimes ambiguous nature, phosphopeptide positional isomers can present challenges in bottom-up mass spectrometry-based workflows as search engine scores alone are often not enough to confidently distinguish them. Additional scoring algorithms can remedy this by providing confidence metrics in addition to these search results, reducing ambiguity. Here we describe challenges to interpreting phosphoproteomics data and review several different approaches to determine sites of phosphorylation for both data-dependent and data-independent acquisition-based workflows. Finally, we discuss open questions regarding neutral losses, gas-phase rearrangement, and false localization rate estimation experienced by both types of acquisition workflows and best practices for managing ambiguity in phosphosite determination.

Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver

Ion mobility coupled to mass spectrometry informs on the shape and size of protein structures in the form of a collision cross section (CCSIM). Although there are several computational methods for predicting CCSIM based on protein structures, including our previously developed projection approximation using rough circular shapes (PARCS), the process usually requires prior experience with the command-line interface. To overcome this challenge, here we present a web application on the Rosetta Online Server that Includes Everyone (ROSIE) webserver to predict CCSIM from protein structure using projection approximation with PARCS. In this web interface, the user is only required to provide one or more PDB files as input. Results from our case studies suggest that CCSIM predictions (with ROSIE-PARCS) are highly accurate with an average error of 6.12%. Furthermore, the absolute difference between CCSIM and CCSPARCS can help in distinguishing accurate from inaccurate AlphaFold2 protein structure predictions. ROSIE-PARCS is designed with a user-friendly interface, is available publicly and is free to use. The ROSIE-PARCS web interface is supported by all major web browsers and can be accessed via this link (https://rosie.graylab.jhu.edu).

Matrix-Assisted Laser Desorption and Electrospray Ionization Tandem Mass Spectrometry of Microbial and Synthetic Biodegradable Polymers

The in-depth structural and compositional investigation of biodegradable polymeric materials, neat or partly degraded, is crucial for their successful applications. Obviously, an exhaustive structural analysis of all synthetic macromolecules is essential in polymer chemistry to confirm the accomplishment of a preparation procedure, identify degradation products originating from side reactions, and monitor chemical-physical properties. Advanced mass spectrometry (MS) techniques have been increasingly applied in biodegradable polymer studies with a relevant role in their further development, valuation, and extension of application fields. However, single-stage MS is not always sufficient to identify unambiguously the polymer structure. Thus, tandem mass spectrometry (MS/MS) has more recently been employed for detailed structure characterization and in degradation and drug release monitoring of polymeric samples, among which are biodegradable polymers. This review aims to run through the investigations carried out by the soft ionization technique matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) MS/MS in biodegradable polymers and present the resulting information.

Advances and Trends in Omics Technology Development

The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

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.

Coupling 193 nm Ultraviolet Photodissociation and Ion Mobility for Sequence Characterization of Conformationally-Selected Peptides

Ultraviolet photodissociation (UVPD) has emerged as a useful technique for characterizing peptide, protein, and protein complex primary and secondary structure. 193 nm UVPD, specifically, enables extensive covalent fragmentation of the peptide backbone without the requirement of a specific side chain chromophore and with no precursor charge state dependence. We have modified a commercial quadrupole-ion mobility-time-of-flight (Q-IM-TOF) mass spectrometer to include 193 nm UVPD following ion mobility. Ion mobility (IM) is a gas-phase separation technique that enables separation of ions by their size, shape, and charge, providing an orthogonal dimension of separation to mass analysis. Following instrument modifications, we characterized the performance of, and information that could be generated from, this new setup using the model peptides substance P, melittin, and insulin chain B. These experiments show extensive fragmentation across the peptide backbone and a variety of ion types as expected from 193 nm UVPD. Additionally, y-2 ions (along with complementary a+2 and b+2 ions) N-terminal to proline were observed. Combining the IM separation and mobility gating capabilities with UVPD, we demonstrate the ability to accomplish both mass- and mobility-selection of bradykinin des-Arg9 and des-Arg1 peptides followed by complete sequence characterization by UVPD. The new capabilities of this modified instrument demonstrate the utility of combining IM with UVPD because isobaric species cannot be independently selected with a traditional quadrupole alone.

Synchrotron UV photoactivation of trapped sodiated ions produced from poly(ethylene glycol) by electrospray ionization

RATIONALE

By taking advantage of the gas-phase decompositions of polymer ions, tandem mass spectrometry of polymers allows us to obtain more accurate structural information than from a simple mass measurement. Applied to a model polymer, the goal of this work was to evaluate the performances of an activation technique based on ultraviolet (UV) irradiation, as an alternative to conventional collisional activation.

METHODS

Sodiated poly(ethylene glycol) produced by electrospray ionization was isolated in a linear ion trap, then submitted to synchrotron UV irradiation over a range of wavelengths (52 to 248 nm). Fragmentation pathways resulting from UV photoactivation were investigated. The proposed mechanisms take into account: (i) the comparison with collision-induced dissociation (CID) product ions, (ii) the effect of wavelength-tunable UV activation, and (iii) deuterium-labeling and various other complementary experiments. For the highest molecular weight compounds, ion mobility spectrometry was used before UV photoactivation.

RESULTS

Synchrotron UV irradiation can induce dissociation of poly(ethylene glycol) sodiated ions without the requirement of the presence of a specific chromophore, if the photon energy is above 10 eV. UV photoactivation of poly(ethylene glycol) ions can yield fragmentations that differ from those in classical low-energy CID, especially from higher masses (>4000 g mol^-1 ). A successful coupling of UV photoactivation with ion mobility pre-filtering was presented.

CONCLUSIONS

UV activation combined or not with pre-filtering ion mobility is a promising alternative approach for the structural characterization of polymers. UV synchrotron radiation with a tunable wavelength was a great opportunity to study the effect of the photon energy, and to probe the mechanisms of ion decomposition from poly(ethylene glycol).

Dipole-Supported Electronic Resonances Mediate Electron-Induced Amide Bond Cleavage

Dissociative electron attachment (DEA) plays a key role in radiation damage of biomolecules under high-energy radiation conditions. The initial step in DEA is often rationalized in terms of resonant electron capture into one of the metastable valence states of a molecule followed by its fragmentation. Our combined theoretical and experimental investigations indicate that the manifold of states responsible for electron capture in the DEA process can be dominated by core-excited (shake-up) dipole-supported resonances. Specifically, we present the results of experimental and computational studies of the gas-phase DEA to three prototypical peptide molecules, formamide, N-methylformamide (NMF), and N,N-dimethyl-formamide (DMF). In contrast to the case of electron capture by positively charged peptides in which amide bond rupture is rare compared to N─C_{α} bond cleavage, fragmentation of the amide bond was observed in each of these three molecules. The ion yield curves for ions resulting from this amide bond cleavage, such as NH_{2}^{-} for formamide, NHCH_{3}^{-} for NMF, and N(CH_{3})_{2}^{-} for DMF, showed a double-peak structure in the region between 5 and 8 eV. The peaks are assigned to Feshbach resonances including core-excited dipole-supported resonances populated upon electron attachment based on high-level electronic structure calculations. Moreover, the lower energy peak is attributed to formation of the core-excited resonance that correlates with the triplet state of the neutral molecule. The latter process highlights the role of optically spin-forbidden transitions promoted by electron impact in the DEA process.

[Site-specific O-Glycosylation Analysis of Therapeutic Fc-fusion Protein by Mass Spectrometry]

Therapeutic Fc-fusion proteins, created by linking bioactive peptides or receptor proteins to the Fc moiety of IgG, are currently being developed. In this development process, a Gly-Gly-Gly-Ser linker (G4S linker) is often used to link the peptide/protein and the Fc portion. O-xylose-type core glycans of glycosaminoglycan are known to attach to the Ser residue on the GSG motif in the G4S linker peptide repeats of the Fc fusion protein produced using the Chinese hamster ovary (CHO) cell expression system. In addition, a recent report demonstrated that unexpected mucin-type O-glycosylations occurred on a peptide in a bioactive peptide-Fc fusion protein; this glycosylation affected the bioactivity of the peptide. Therapeutic proteins with non-natural structures, such as Fc-fusion proteins, undergo unintended O-glycosylations; therefore, it is increasingly important to conduct detailed O-glycosylation analysis of fusion proteins during the developmental stages. In this paper, we have summarized recent reports on the unexpected O-glycosylation in fusion proteins, general O-glycosylation types and sequence motifs, and O-glycosylation analytical techniques involving O-linked oligosaccharide analysis and site-specific O-glycosylation analysis using LC/MS. In addition, we have introduced site-specific O-glycosylation analysis of Fc-fusion proteins with GS linker peptides by LC/MS using higher-energy collisional dissociation-tandem mass spectrometry (HCD-MS/MS) and electron-transfer dissociation (ETD)-MS/MS to obtain preferential dissociation of the peptide moiety in the glycopeptide.

GPU Assisted Simulation Study of Ion-Ion Reactions within Quadrupole Ion Traps

In this study, a gas-phase ion-ion reaction model was developed, and it was integrated into an ion trajectory simulation program. GPU parallel computation techniques were also applied to accelerate the simulation process. With this simulation tool, the dependence of ion-ion reaction rate within 3D quadrupole ion traps on both ion trap operation parameters and the characteristics of reaction pair were investigated. It was found that the m/z values and charge states of ions have significant influences on the reaction rate. Moreover, higher ion-ion reaction rate was achieved under higher trapping voltages and higher buffer gas pressures. Furthermore, secondary reaction and/or neutralization of ETD fragment ions were observed from simulation. The reaction and/or neutralization rate depends on the charge state and m/z of each fragment ion.

Solid-state NMR studies of Ziegler-Natta and metallocene catalysts

Ziegler-Natta catalysts are the workhorses of polyolefin production. However, although they have been used and intensively studied for half a century, there is still no comprehensive picture of their mechanistic operation. New techniques are needed to gain more insight in these catalysts. Solid-state NMR has reached a high level of sophistication over the last few decades and holds great promise for providing a deeper insight in Ziegler-Natta catalysis. This review outlines the possibilities for solid-state NMR to characterize the different components and interactions in Ziegler-Natta and metallocene catalysts. An overview is given of some of the expected mechanisms and the resulting polymer microstructure and other characteristics. In the second part of this review we present studies that have used solid-state NMR to investigate the composition of Ziegler-Natta and metallocene catalysts or the interactions between their components.

Electron transfer dissociation of doubly charged ions with different cationizing agents

Electron transfer dissociation (ETD) studies have been performed on a peptide and a synthetic polysaccharide doubly charged by different cationization agents. The ETD of protonated-sodiated bombesin gave rise to contiguous series of abundant c- and z-type ions that identified the complete sequence. ETD of the doubly protonated peptide produced a different fragment distribution, which also allowed for complete sequence coverage, but the relative intensities of some sequence ions were very small. Collisionally activated dissociation (CAD) of either precursor rendered limited sequence information. ETD of the sodiated-ammoniated pentamer of a starch-derived linear polysaccharide caused extensive fragmentation through cross-ring cleavages that revealed the possible position of a hydroxyethyl substituent on the saccharide ring. In contrast, ETD of the di-sodiated pentasaccharide did not produce a structure-revealing fragmentation pattern. On the other hand, CAD resulted in efficient glycosidic bond cleavages, either directly (from the sodiated-ammoniated precursor) or via multi-stage fragmentation (from the di-sodiated precursor), which indicated that hydroxyethylation occurs randomly at any saccharide repeat unit along the chain. Overall, the use of different cationizing agents complements the information available by using identical charge sites and opens or enhances ETD pathways that unveil valuable sequence or positional information.