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1. Capillary Zone Electrophoresis-Electron-Capture Collision-Induced Dissociation on a Quadrupole Time-of-Flight Mass Spectrometer for Top-Down Characterization of Intact Proteins

   https://doi.org/10.1021/jasms.0c00484  

   Shen, Xiaojing; Xu, Tian; Hakkila, Blake; Hare, Mike; Wang, Qianjie; Wang, Qianyi; Beckman, Joseph S.; Sun, Liangliang (March 2021, Journal of the American Society for Mass Spectrometry)

   null (Ed.)

   Mass spectrometry (MS)-based denaturing top-down proteomics (dTDP) requires high-capacity separation and extensive gas-phase fragmentation of proteoforms. Herein, we coupled capillary zone electrophoresis (CZE) to electron-capture collision-induced dissociation (ECciD) on an Agilent 6545 XT quadrupole time-of-flight (Q-TOF) mass spectrometer for dTDP for the first time. During ECciD, the protein ions were first fragmented using ECD, followed by further activation and fragmentation by applying a CID potential. In this pilot study, we optimized the CZE-ECciD method for small proteins (lower than 20 kDa) regarding the charge state of protein parent ions for fragmentation and the CID potential applied to maximize the protein backbone cleavage coverage and the number of sequence-informative fragment ions. The CZE-ECciD Q-TOF platform provided extensive backbone cleavage coverage for three standard proteins lower than 20 kDa from only single charge states in a single CZE-MS/MS run in the targeted MS/MS mode, including ubiquitin (97%, +7, 8.6 kDa), superoxide dismutase (SOD, 87%, +17, 16 kDa), and myoglobin (90%, +16, 17 kDa). The CZE-ECciD method produced comparable cleavage coverage of small proteins (i.e., myoglobin) with direct-infusion MS studies using electron transfer dissociation (ETD), activated ion-ETD, and combinations of ETD and collision-based fragmentation on high-end orbitrap mass spectrometers. The results render CZE-ECciD a new tool for dTDP to enhance both separation and gas-phase fragmentation of proteoforms. 

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2. Negative-Ion Electron Capture Dissociation of MALDI-Generated Peptide Anions

   https://doi.org/10.1021/acs.analchem.4c01292  

   DeFiglia, Steven A; Szot, Carson W; Håkansson, Kristina (May 2024, Analytical Chemistry)

   Negative-ion electron capture dissociation (niECD) is an anion MS/MS technique that provides fragmentation analogous to conventional ECD, including high peptide sequence coverage and retention of labile post-translational modifications (PTMs). niECD has been proposed to be the most efficient for salt-bridged zwitterionic precursor ion structures. Several important PTMs, e.g., sulfation and phosphorylation, are acidic and can, therefore, be challenging to characterize in the positive-ion mode. Furthermore, PTM-friendly techniques, such as ECD, require multiple precursor ion-positive charges. By contrast, singly charged ions, refractory to ECD, are most compatible with niECD. Because electrospray ionization (ESI) typically yields multiply charged ions, we sought to explore matrix-assisted laser desorption/ionization (MALDI) in combination with niECD. However, the requirement for zwitterionic gaseous structures may preclude efficient niECD of MALDI-generated anions. Unexpectedly, we found that niECD of anions from MALDI is not only possible but proceeds with similar or higher efficiency compared with ESI-generated anions. Matrix selection did not appear to have a major effect. With MALDI, niECD is demonstrated up to m/z ∼4300. For such larger analytes, multiple electron captures are observed, resulting in triply charged fragments from singly charged precursor ions. Such charge-increased fragments show improved detectability. Furthermore, significantly improved (∼20-fold signal-to-noise increase) niECD spectral quality is achieved with equivalent sample amounts from MALDI vs ESI. Overall, the reported combination with MALDI significantly boosts the analytical utility of niECD. 

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3. Salt-Bridged Peptide Anion Gaseous Structures Enable Efficient Negative Ion Electron Capture Dissociation

   https://doi.org/10.1021/jasms.4c00030  

   Wang, Ning; Dixit, Sugyan M; Lee, Teresa; DeFiglia, Steven A; Ruotolo, Brandon T; Håkansson, Kristina (April 2024, Journal of the American Society for Mass Spectrometry)

   We previously discovered that electron attachment to gaseous peptide anions can occur within a relatively narrow electron energy range. The resulting charge-increased radical ions undergo dissociation analogous to conventional cation electron capture/transfer dissociation (ECD/ETD), thus enabling a novel tandem mass spectrometry (MS/MS) technique that we termed negative ion electron capture dissociation (niECD). We proposed that gaseous zwitterionic structures are required for niECD with electron capture either occurring at or being directed by a positively charged site. Here, we further evaluate this zwitterion mechanism by performing niECD of peptides derivatized to alter their ability to form zwitterionic gaseous structures. Introduction of a fixed positive charge tag, a highly basic guanidino group, or a highly acidic sulfonate group to promote zwitterionic structures in singly charged anions, rescued the niECD ability of a peptide refractory to niECD in its unmodified form. We also performed a systematic study of five sets of synthetic peptides with decreasing zwitterion propensity and found that niECD efficiency decreased accordingly, further supporting the zwitterion mechanism. However, traveling-wave ion mobility-mass spectrometry experiments, performed to gain further insight into the gas-phase structures of peptides showing high niECD efficiency, exhibited an inverse correlation between the orientationally averaged collision cross sections and niECD efficiency. These results indicate that compact salt-bridged structures are also a requirement for effective niECD. 

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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. Extraction anode lens effects in gas phase peptide cation-electron reactions

   https://doi.org/10.1016/j.ijms.2024.117390  

   DeFiglia, Steven A; Lee, Teresa; Mikawy, Neven N; Szot, Carson W; Håkansson, Kristina (March 2025, International Journal of Mass Spectrometry)

   Gas phase cation-electron reactions, from electron capture dissociation (ECD; <1 eV electrons) to electron ionization dissociation (>~26 eV electrons), are highly beneficial for biomolecular structural characterization. These techniques offer high sequence coverage, labile posttranslational modification retention, and sidechain loss fragments which can differentiate isomeric residues. For optimum performance, careful tuning of electron energy, flux, and irradiation time is required to reach efficiency at a particular energy regime. The cathode bias voltage (CBV) is the primary determinant of electron energy, while several parameters including CBV, extraction anode lens voltage (LV), and cathode heating current determine electron flux. We present an in-depth examination of how the interplay of these parameters at variable irradiation times results in differing peptide cation-electron reaction regimes. A particularly interesting finding was the prominent high energy fragmentation pathways observed at low (~- 1.0 V) CBV and high (>50 V) LV, as compared with conventional (~5 V) LV for peptide ECD. Specifically, high LV resulted in tandem ionization, observed for both singly- and doubly protonated peptides, alongside increased sequence coverage for both charge states from complex spectra containing a multitude of a/b/c/d/w/x/y/z•-type terminal fragments as well as internal fragments and a large number of neutral losses. Electron flux and energy measurements as well as electron irradiation at constant flux showed that an increased number of higher energy electrons are present at high vs. low LV, i.e., the observed “lens effect” is likely due to the presence of high energy electrons under such conditions. This extraction anode lens effect may explain previous observations of unexpected internal fragments from ECD. 

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