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1. Understanding the structural complexity of dissolved organic matter: isomeric diversity

   https://doi.org/10.1039/c8fd00221e  

   Leyva, Dennys; Tose, Lilian V.; Porter, Jacob; Wolff, Jeremy; Jaffé, Rudolf; Fernandez-Lima, Francisco (August 2019, Faraday Discussions)

   In the present work, the advantages of ESI-TIMS-FT-ICR MS to address the isomeric content of dissolved organic matter are studied. While the MS spectra allowed the observation of a high number of peaks ( e.g. , PAN-L: 5004 and PAN-S: 4660), over 4× features were observed in the IMS-MS domain ( e.g. , PAN-L: 22 015 and PAN-S: 20 954). Assuming a total general formula of C x H y N 0–3 O 0–19 S 0–1 , 3066 and 2830 chemical assignments were made in a single infusion experiment for PAN-L and PAN-S, respectively. Most of the identified chemical compounds (∼80%) corresponded to highly conjugated oxygen compounds (O 1 –O 20 ). ESI-TIMS-FT-ICR MS provided a lower estimate of the number of structural and conformational isomers ( e.g. , an average of 6–10 isomers per chemical formula were observed). Moreover, ESI-q-FT-ICR MS/MS at the level of nominal mass ( i.e. , 1 Da isolation) allowed for further estimation of the number of isomers based on unique fragmentation patterns and core fragments; the later suggested that multiple structural isomers could have very closely related CCS. These studies demonstrate the need for ultrahigh resolution TIMS mobility scan functions ( e.g. , R = 200–500) in addition to tandem MS/MS isolation strategies. 

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2. Metal ions induced secondary structure rearrangements: mechanically interlocked lasso vs. unthreaded branched-cyclic topoisomers

   https://doi.org/10.1039/c8an00138c  

   Jeanne Dit Fouque, Kevin; Moreno, Javier; Hegemann, Julian D.; Zirah, Séverine; Rebuffat, Sylvie; Fernandez-Lima, Francisco (January 2018, The Analyst)

   Metal ions can play a significant role in a variety of important functions in protein systems including cofactor for catalysis, protein folding, assembly, structural stability and conformational change. In the present work, we examined the influence of alkali (Na, K and Cs), alkaline earth (Mg and Ca) and transition (Co, Ni and Zn) metal ions on the conformational space and analytical separation of mechanically interlocked lasso peptides. Syanodin I, sphingonodin I, caulonodin III and microcin J25, selected as models of lasso peptides, and their respective branched-cyclic topoisomers were submitted to native nESI trapped ion mobility spectrometry-mass spectrometry (TIMS-MS). The high mobility resolving power of TIMS permitted to group conformational families regardless of the metal ion. The lower diversity of conformational families for syanodin I as compared to the other lasso peptides supports that syanodin I probably forms tighter binding interactions with metal ions limiting their conformational space in the gas-phase. Conversely, the higher diversity of conformational families for the branched-cyclic topologies further supports that the metal ions probably interact with a higher number of electronegative groups arising from the fully unconstraint C-terminal part. A correlation between the lengths of the loop and the C-terminal tail with the conformational space of lasso peptides becomes apparent upon addition of metal ions. It was shown that the threaded C-terminal region in lasso peptides allows only for distinct interactions of the metal ion with either residues in the loop or tail region. This limits the size of the interacting region and apparently leads to a bias of metal ion binding in either the loop or tail region, depending whichever section is larger in the respective lasso peptide. For branched-cyclic peptides, the non-restricted C-terminal tail allows metal coordination by residues throughout this region, which can result in gas-phase structures that are sometimes even more compact than the lasso peptides. The high TIMS resolution also resulted in the separation of almost all lasso and branched-cyclic topoisomer metal ions ( r ∼ 2.1 on average). It is also shown that the metal incorporation ( e.g. , doubly cesiated species) can lead to the formation of a simplified IMS pattern (or preferential conformers), which results in baseline analytical separation and discrimination between lasso and branched-cyclic topologies using TIMS-MS. 

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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. Tandem trapped ion mobility spectrometry

   https://doi.org/10.1039/c7an02054f  

   Liu, Fanny C.; Ridgeway, Mark E.; Park, Melvin A.; Bleiholder, Christian (January 2018, The Analyst)

   There is currently a strong interest in the use of ion mobility spectrometry-mass spectrometry (IMS-MS) instrumentation for structural biology. In these applications, momentum transfer cross sections derived from IMS-MS measurements are used to reconstruct the three-dimensional analyte structure. Recent reports indicate that additional structural information can be extracted from measuring changes in cross sections in response to changes of the analyte structure. To further this approach, we constructed a tandem trapped IMS analyser (TIMS-TIMS) and incorporated it in a QqTOF mass spectrometer. TIMS-TIMS is constructed by coupling two TIMS analysers via an “interface region” composed of two apertures. We show that peptide oligomers (bradykinin) and native-like protein (ubiquitin) ions can be preserved through the course of an experiment in a TIMS-TIMS analyser. We demonstrate the ability to collisionally-activate as well as to trap mobility-selected ions, followed by subsequent mobility-analysis. In addition to inducing conformational changes, we show that we can fragment low charge states of ubiquitin at >1 mbar between the TIMS analysers with significant sequence coverage. Many fragment ions exhibit multiple features in their TIMS spectra, which means that they may not generally exist as the most stable isomer. The ability of TIMS-TIMS to dissociate mobility-selected protein ions and to measure the cross sections of their fragment ions opens new possibilities for IMS-based structure elucidation. 

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5. Field induced fragmentation spectra from reactive stage-tandem differential mobility spectrometry

   https://doi.org/10.1039/d0an00665c  

   Fowler, P. E.; Pilgrim, J. Z.; Lee, G.; Eiceman, G. A. (July 2020, The Analyst)

   A planar tandem differential mobility spectrometer was integrated with a middle reactive stage to fragment ions which were mobility selected in a first analyzer stage using characteristic compensation and separation fields. Fragmentation occurred in air at ambient pressure of 660 Torr (8.8 kPa) with electric fields of 10 to 35 kV cm −1 (E/N of 52 to 180 Td) between two 1 mm wide metal strips, located on each analyzer plate between the first and second mobility stages. Field induced fragmentation (FIF) spectra were produced by characterizing, in a last stage, the mobilities of fragment ions from protonated monomers of 43 oxygen-containing volatile organic compounds from five chemical classes. The extent of fragmentation was proportional to E/N with alcohols, aldehydes, and ethers undergoing multiples steps of fragmentation; acetates fragmented only to a single ion, protonated acetic acid. In contrast, fragmentation of ketones occurred only for methyl i-butyl ketone and 2-hexanone. Fragment ion identities were supported by mass-analysis and known fragmentation routes and suggested that field induced fragmentation at ambient pressure can introduce structural information into FIF spectra, establishing a foundation for chemical identification using mobility methods. 

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