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1. Charge transfer dissociation of a branched glycan with alkali and alkaline earth metal adducts

   https://doi.org/10.1002/jms.4774  

   Sasiene, Zachary_J; Ropartz, David; Rogniaux, Hélène; Jackson, Glen_P (June 2021, Journal of Mass Spectrometry)

   Abstract Alkali and alkaline earth metal adducts of a branched glycan, XXXG, were analyzed with helium charge transfer dissociation (He‐CTD) and low‐energy collision‐induced dissociation (LE‐CID) to investigate if metalation would impact the type of fragments generated and the structural characterization of the analyte. The studied adducts included 1+ and 2+ precursors involving one or more of the cations: H⁺, Na⁺, K⁺, Ca²⁺, and Mg²⁺. Regardless of the metal adduct, He‐CTD generated abundant and numerous glycosidic and cross‐ring cleavages that were structurally informative and able to identify the 1,4‐linkage and 1,6‐branching patterns. In contrast, the LE‐CID spectra mainly contained glycosidic cleavages, consecutive fragments, and numerous neutral losses, which complicated spectral interpretation. LE‐CID of [M + K + H]²⁺and [M + Na]⁺precursors generated a few cross‐ring cleavages, but they were not sufficient to identify the 1,4‐linkage and 1,6‐branching pattern of the XXXG xyloglucan. He‐CTD predominantly generated 1+ fragments from 1+ precursors and 2+ product ions from 2+ precursors, although both LE‐CID and He‐CTD were able to generate 1+ product ions from 2+ adducts of magnesium and calcium. The singly charged fragments derive from the loss of H⁺from the metalated product ions and the formation of a protonated complementary product ion; such observations are similar to previous reports for magnesium and calcium salts undergoing electron capture dissociation (ECD) activation. However, during He‐CTD, the [M + Mg]²⁺precursor generated more singly charged product ions than [M + Ca]²⁺, either because Mg has a higher second ionization potential than Ca or because of conformational differences and the locations of the charging adducts during fragmentation. He‐CTD of the [M + 2Na]²⁺and the [M + 2 K]²⁺precursors generated singly charged product ions from the loss of a sodium ion and potassium ion, respectively. In summary, although the metal ions influence the mass and charge state of the observed product ions, the metal ions had a negligible effect on the types of cross‐ring cleavages observed. 

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2. A plethora of isomerization processes and hydrogen scrambling in the fragmentation of the methanol dimer cation: a PEPICO study

   https://doi.org/10.1039/d1cp05155e  

   Wu, Xiangkun; Zhou, Xiaoguo; Bjelić, Saša; Hemberger, Patrick; Sztáray, Bálint; Bodi, Andras (January 2022, Physical Chemistry Chemical Physics)

   The valence photoionization of light and deuterated methanol dimers was studied by imaging photoelectron photoion coincidence spectroscopy in the 10.00–10.35 eV photon energy range. Methanol clusters were generated in a rich methanol beam in nitrogen after expansion into vacuum. They generally photoionize dissociatively to protonated methanol cluster cations, (CH 3 OH) n H + . However, the stable dimer parent ion (CH 3 OH) 2 + is readily detected below the dissociation threshold to yield the dominant CH 3 OH 2 + fragment ion. In addition to protonated methanol, we could also detect the water- and methyl-loss fragment ions of the methanol dimer cation for the first time. These newly revealed fragmentation channels are slow and cannot compete with protonated methanol cation formation at higher internal energies. In fact, the water- and methyl-loss fragment ions appear together and disappear at a ca. 150 meV higher energy in the breakdown diagram. Experiments with selectively deuterated methanol samples showed H scrambling involving two hydroxyl and one methyl hydrogens prior to protonated methanol formation. These insights guided the potential energy surface exploration to rationalize the dissociative photoionization mechanism. The potential energy surface was further validated by a statistical model including isotope effects to fit the experiment for the light and the perdeuterated methanol dimers simultaneously. The (CH 3 OH) 2 + parent ion dissociates via five parallel channels at low internal energies. The loss of both CH 2 OH and CH 3 O neutral fragments leads to protonated methanol. However, the latter, direct dissociation channel is energetically forbidden at low energies. Instead, an isomerization transition state is followed by proton transfer from a methyl group, which leads to the CH 3 (H)OH + ⋯CH 2 OH ion, the precursor to the CH 2 OH-, H 2 O-, and CH 3 -loss fragments after further isomerization steps, in part by a roaming mechanism. Water loss yields the ethanol cation, and two paths are proposed to account for m/z 49 fragment ions after CH 3 loss. The roaming pathways are quickly outcompeted by hydrogen bond breaking to yield CH 3 OH 2 + , which explains the dominance of the protonated methanol fragment ion in the mass spectrum. 

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3. Are Internal Fragments Observable in Electron Based Top-Down Mass Spectrometry?

   https://doi.org/10.1016/j.mcpro.2024.100814  

   Mikawy, Neven N; Rojas_Ramírez, Carolina; DeFiglia, Steven A; Szot, Carson W; Le, Jessie; Lantz, Carter; Wei, Benqian; Zenaidee, Muhammad A; Blakney, Greg T; Nesvizhskii, Alexey I; et al (September 2024, Molecular & Cellular Proteomics)

   Protein tandem mass spectrometry (MS/MS) often generates sequence-informative fragments from backbone bond cleavages near the termini. This lack of fragmentation in the protein interior is particularly apparent in native top-down MS. Improved sequence coverage, critical for reliable annotation of posttranslational modifications (PTMs) and sequence variants, may be obtained from internal fragments generated by multiple backbone cleavage events. However, internal fragment assignments can be error prone due to isomeric/isobaric fragments from different parts of a protein sequence. Also, internal fragment generation propensity depends on the chosen MS/MS activation strategy. Here, we examine internal fragment formation in electron capture dissociation (ECD) and electron transfer dissociation (ETD) following native and denaturing MS, as well as liquid chromatography (LC)/MS of several proteins. Experiments were undertaken on multiple instruments, including Q-ToF, Orbitrap, and high-field FT-ICR across four laboratories. ECD was performed at both ultrahigh vacuum and at similar pressure to ETD conditions. Two complementary software packages were used for data analysis. When feasible, ETD-higher-energy collision dissociation (ETD-HCD) MS3 was performed to validate/refute potential internal fragment assignments, including differentiating MS3 fragmentation behavior of radical vs. even-electron primary fragments. We show that, under typical operating conditions, internal fragments cannot be confidently assigned in ECD, nor ETD. On the other hand, such fragments, along with some b-type terminal fragments (not typically observed in ECD/ETD spectra) appear at atypical ECD operating conditions, suggesting they originate from a separate ion-electron activation process. Furthermore, atypical fragment ion types, e.g., x ions, are observed at such conditions as well as upon EThcD, presumably due to vibrational activation of radical z-type ions. 

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4. Deprotonated carbohydrate anion fragmentation chemistry: structural evidence from tandem mass spectrometry, infra-red spectroscopy, and theory

   https://doi.org/10.1039/C8CP02620C  

   Rabus, Jordan M.; Simmons, Daniel R.; Maître, Philippe; Bythell, Benjamin J. (November 2018, Physical Chemistry Chemical Physics)

   We investigate the gas-phase structures and fragmentation chemistry of deprotonated carbohydrate anions using combined tandem mass spectrometry, infrared spectroscopy, regioselective labelling, and theory. Our model system is deprotonated, [lactose-H] − . We computationally characterize the rate-determining barriers to glycosidic bond (C 1 –Z 1 reactions) and cross-ring cleavages, and compare these predictions to our tandem mass spectrometric and infrared spectroscopy data. The glycosidic bond cleavage product data support complex mixtures of anion structures in both the C 1 and Z 1 anion populations. The specific nature of these distributions is predicted to be directly affected by the nature of the anomeric configuration of the precursor anion and the distribution of energies imparted. i.e. , Z 1 anions produced from the β-glucose anomeric form have a differing distribution of product ion structures than do those from the α-glucose anomeric form. The most readily formed Z 1 anions ([1,4-anhydroglucose-H] − structures) are produced from the β-glucose anomers, and do not ring-open and isomerize as the hemiacetal group is no longer present. In contrast the [3,4-anhydroglucose-H] − , Z 1 anion structures, which are most readily produced from α-glucose forms, can ring-open through very low barriers (<25 kJ mol −1 ) to form energetically and entropically favorable aldehyde isomers assigned with a carbonyl stretch at ∼1640 cm −1 . Barriers to interconversion of the pyranose [β-galactose-H] − , C 1 anions to ring-open forms were larger, but still modest (≥51 kJ mol −1 ) consistent with evidence of the presence of both forms in the infrared spectrum. For the cross-ring cleavage 0,2 A 2 anions, ring-opening at the glucose hemiacetal of [lactose-H] − is rate-limiting (>180 (α-), >197 kJ mol −1 (β-anomers)). This finding offers an explanation for the low abundance of these product anions in our tandem mass spectra. 

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5. Decoding the Fucose Migration Product during Mass‐Spectrometric analysis of Blood Group Epitopes

   https://doi.org/10.1002/anie.202302883  

   Lettow, Maike; Greis, Kim; Mucha, Eike; Lambeth, Tyler R.; Yaman, Murat; Kontodimas, Vasilis; Manz, Christian; Hoffmann, Waldemar; Meijer, Gerard; Julian, Ryan R.; et al (May 2023, Angewandte Chemie International Edition)

   Abstract Fucose is a signaling carbohydrate that is attached at the end of glycan processing. It is involved in a range of processes, such as the selectin‐dependent leukocyte adhesion or pathogen‐receptor interactions. Mass‐spectrometric techniques, which are commonly used to determine the structure of glycans, frequently show fucose‐containing chimeric fragments that obfuscate the analysis. The rearrangement leading to these fragments—often referred to as fucose migration—has been known for more than 25 years, but the chemical identity of the rearrangement product remains unclear. In this work, we combine ion‐mobility spectrometry, radical‐directed dissociation mass spectrometry, cryogenic IR spectroscopy of ions, and density‐functional theory calculations to deduce the product of the rearrangement in the model trisaccharides Lewis x and blood group H2. The structural search yields the fucose moiety attached to the galactose with anα(1→6) glycosidic bond as the most likely product. 

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