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1. 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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2. Analysis of Fentanyl and Fentanyl Analogs Using Atmospheric Pressure Chemical Ionization Gas Chromatography–Mass Spectrometry (APCI-GC-MS)

   https://doi.org/10.1021/jasms.4c00455  

   Reyes_Monroy, Karen A; McCrary, Richard; Parry, Isabelle; Webber, Catherine; Golden, Teresa D; Verbeck, Guido F (March 2025, Journal of the American Society for Mass Spectrometry)

   Illicit fentanyl and fentanyl analogs are a growing concern in the United States as opioid related deaths rise. Given that fentanyl analogs are readily obtained by modifying the structure of fentanyl, illicit fentanyl analogs appearing on the black market often contain similar structures, making analogue differentiation and identification difficult. Thus, obtaining both precursor and product ion data during analysis is becoming increasingly valuable in fentanyl analog characterization. In this paper, we provide GC column retention time, precursor, and product ion mass spectrum data for 74 fentanyl analogs that were analyzed using atmospheric pressure chemical ionization-gas chromatography−mass spectrometry (APCI-GC-MS) utilizing a triple quadrupole mass analyzer. During analysis, precursor ions underwent collision induced dissociation (CID) by increasing the collision energy (10, 20, 30, 40, and 50 V) throughout a single run. Data reveal that APCI readily produces product ions of the piperidine and N-alkyl chain but rarely provides data on the acyl group. Furthermore, fentanyl analogs with greater substitution at the N-alkyl chain demonstrate a greater preference for dissociation at the N-αC and αC-βC bond, while greater substitution at the amide group leads to fragmentation at the N−C4 bond. 

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3. Tandem mass spectrometry using continuous‐wave infrared multiphoton dissociation in an electrostatic linear ion trap

   https://doi.org/10.1002/rcm.9698  

   Carrick, Ian_J; Fabijanczuk, Kimberly_C; Rong, Jiayue; McLuckey, Scott_A (January 2024, Rapid Communications in Mass Spectrometry)

   RationaleThe electrostatic linear ion trap (ELIT) can be operated as a multi‐reflection time‐of‐flight (MR‐TOF) or Fourier transform (FT) mass analyzer. It has been shown to be capable of performing high‐resolution mass analysis and high‐resolution ion isolations. Although it has been used in charge‐detection mass spectrometry (CDMS), it has not been widely used as a conventional mass spectrometer for ensemble measurements of ions, or for tandem mass spectrometer. The advantages of tandem mass spectrometer with high‐resolution ion isolations in the ELIT have thus not been fully exploited. MethodsA homebuilt ELIT was modified with BaF₂viewports to facilitate transmission of a laser beam at the turnaround point of the second ion mirror in the ELIT. Fragmentation that occurs at the turnaround point of these ion mirrors should result in minimal energy partitioning due to the low kinetic energy of ions at these points. The laser was allowed to irradiate ions for a period of many oscillations in the ELIT. ResultsDue to the low energy absorption of gas‐phase ions during each oscillation in the ELIT, fragmentation was found to occur over a range of oscillations in the ELIT generating a homogeneous ion beam. A mirror‐switching pulse is shown to create time‐varying perturbations in this beam that oscillate at the fragment ion characteristic frequencies and generate a time‐domain signal. This was found to recover FT signal for protonated pYGGFL and pSGGFL precursor ions. ConclusionsFragmentation at the turnaround point of an ELIT by continuous‐wave infrared multiphoton dissociation (cw‐IRMPD) is demonstrated. In cases where laser power absorption is low and fragmentation occurs over many laps, a mirror‐switching pulse may be used to recover varying time‐domain signal. The combination of laser activation at the turnaround points and mirror‐switching isolation allows for tandem MS in the ELIT. 

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4. Effective discrimination of gas-phase peptide conformers using TIMS-ECD-ToF MS/MS

   https://doi.org/10.1039/d1ay01461g  

   Jeanne Dit Fouque, K.; Wellmann, M.; Leyva Bombuse, D.; Santos-Fernandez, M.; Cintron-Diaz, Y. L.; Gomez-Hernandez, M. E.; Kaplan, D.; Voinov, V. G.; Fernandez-Lima, F. (November 2021, Analytical Methods)

   In the present work, four, well-studied, model peptides ( e.g. , substance P, bradykinin, angiotensin I and AT-Hook 3) were used to correlate structural information provided by ion mobility and ECD/CID fragmentation in a TIMS-q-EMS-ToF MS/MS platform, incorporporating an electromagnetostatic cell (EMS). The structural heterogeneity of the model peptides was observed by (i) multi-component ion mobility profiles (high ion mobility resolving power, R ∼115–145), and (ii) fast online characteristic ECD fragmentation patterns per ion mobility band (∼0.2 min). Particularly, it was demonstrated that all investigated species were probably conformers, involving cis / trans -isomerizations at X-Pro peptide bond, following the same protonation schemes, in good agreement with previous ion mobility and single point mutation experiments. The comparison between ion mobility selected ECD spectra and traditional FT-ICR ECD MS/MS spectra showed comparable ECD fragmentation efficiencies but differences in the ratio of radical (˙)/prime (′) fragment species (H˙ transfer), which were associated with the differences in detection time after the electron capture event. The analysis of model peptides using online TIMS-q-EMSToF MS/MS provided complementary structural information on the intramolecular interactions that stabilize the different gas-phase conformations to those obtained by ion mobility or ECD alone. 

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5. 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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