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1. Differentiating aspartic acid isomers and epimers with charge transfer dissociation mass spectrometry (CTD-MS)

   https://doi.org/10.1039/D1AN02279B  

   Edwards, Halle M. ; Wu, Hoi-Ting ; Julian, Ryan R. ; Jackson, Glen P. ( March 2022 , The Analyst)

   The ability to understand the function of a protein often relies on knowledge about its detailed structure. Sometimes, seemingly insignificant changes in the primary structure of a protein, like an amino acid substitution, can completely disrupt a protein's function. Long-lived proteins (LLPs), which can be found in critical areas of the human body, like the brain and eye, are especially susceptible to primary sequence alterations in the form of isomerization and epimerization. Because long-lived proteins do not have the corrective regeneration capabilities of most other proteins, points of isomerism and epimerization that accumulate within the proteins can severely hamper their functions and can lead to serious diseases like Alzheimer's disease, cancer and cataracts. Whereas tandem mass spectrometry (MS/MS) in the form of collision-induced dissociation (CID) generally excels at peptide characterization, MS/MS often struggles to pinpoint modifications within LLPs, especially when the differences are only isomeric or epimeric in nature. One of the most prevalent and difficult-to-identify modifications is that of aspartic acid between its four isomeric forms: l -Asp, l -isoAsp, d -Asp, and d -isoAsp. In this study, peptides containing isomers of Asp were analyzed by charge transfer dissociation (CTD) mass spectrometry to identify spectral features that could discriminatemore »between the different isomers. For the four isomers of Asp in three model peptides, CTD produced diagnostic ions of the form c n +57 on the N-terminal side of iso-Asp residues, but not on the N-terminal side of Asp residues. Using CTD, the l - and d forms of Asp and isoAsp could also be differentiated based on the relative abundance of y - and z ions on the C-terminal side of Asp residues. Differentiation was accomplished through a chiral discrimination factor, R , which compares an ion ratio in a spectrum of one epimer or isomer to the same ion ratio in the spectrum of a different epimer or isomer. The R values obtained using CTD are as robust and statistically significant as other fragmentation techniques, like radical directed dissociation (RDD). In summary, the extent of backbone and side-chain fragments produced by CTD enabled the differentiation of isomers and epimers of Asp in a variety of peptides.« less
2. Resolving Isomers of Star-Branched Poly(Ethylene Glycols) by IMS-MS Using Multiply Charged Ions

   https://doi.org/10.1021/jasms.0c00045  

   Austin, Calvin A. ; Inutan, Ellen D. ; Bohrer, Brian C. ; Li, Jing ; Fischer, Joshua L. ; Wijerathne, Kanchana ; Foley, Casey D. ; Lietz, Christopher B. ; Woodall, Daniel W. ; Imperial, Lorelie F. ; et al ( January 2020 , Journal of the American Society for Mass Spectrometry)

   Ion mobility spectrometry (IMS) mass spectrometry (MS) centers on the ability to separate gaseous structures by size, charge, shape, and followed by mass-to-charge (m/z). For oligomeric structures, improved separation is hypothesized to be related to the ability to extend structures through repulsive forces between cations electrostatically bonded to the oligomers. Here we show the ability to separate differently branched multiply charged ions of star-branched poly(ethylene glycol) oligomers (up to 2000 Da) regardless of whether formed by electrospray ionization (ESI) charged solution droplets or from charged solid particles produced directly from a surface by matrix-assisted ionization. Detailed structural characterization of isomers of the star-branched compositions was first established using a home-built high-resolution ESI IMS-MS instrument. The doubly charged ions have well-resolved drift times, achieving separation of isomers and also allowing differentiation of star-branched versus linear oligomers. An IMS-MS “snapshot” approach allows visualization of architectural dispersity and (im)purity of samples in a straightforward manner. Analyses capabilities are shown for different cations and ionization methods using commercially available traveling wave IMS-MS instruments. Analyses directly from surfaces using the new ionization processes are, because of the multiply charging, not only associated with the benefits of improved gas-phase separations, relative to that of ions producedmore »by matrix-assisted laser desorption/ionization, but also provide the potential for spatially resolved measurements relative to ESI and other ionization methods.« less
3. Increasing Confidence in Resolving Isomers of Emerging Per-And Polyfluoroalkyl Substances (PFASs) by Using DFT and Cosmo-Rs to Predict Chromatographic Retention Factors

   Antle, J. ; Guardin, M.G. ; Aga, D. ; Simpson, S. ( May 2022 , Annual meeting abstracts)

   Per-and polyfluoroalkyl substances (PFAS) are a class of contaminants of emerging concern frequently used in products like aqueous firefighting foams and non-stick coatings due to their stability and surfactant-like qualities. The lack of analytical standards for many emerging PFAS have severely limited our ability to comprehensively identify unknown PFAS contaminants in the environment, especially those that occur as isomers. Annotation of small molecules and identification of unknowns based only on elemental composition and mass fragmentation patterns remain major challenges in nontarget analysis employing liquid chromatography with high-resolution mass spectrometry (LC-HRMS). In this study, chromatographic retention factors (k) and mass spectral fragmentation patterns of 32 known PFAS were determined using our optimized parameters in LC-HRMS. The same method was then used to analyze previously unidentified PFAS in actual environmental samples. Using characteristic ions observed in the MS fragmentation of PFAS, the most probable isomeric structures of the detected PFAS were predicted. To increase confidence in the predicted molecular structure, Density Functional Theory and Conductor-like Screening Model for Realistic Solvents (COSMO-RS) calculations were used to predict physicochemical properties of different constitutional isomers. The DFT calculations facilitated geometric optimization, determination of polarizability, and calculation of the chemical potential the isomers. COSMO-RS uses themore »chemical potential to predict thermodynamic properties of molecules such as pKa, solubility, and Kow. These properties were then used to make a multi-variable linear regression to predict k values. The model was trained using 32 known PFAS. The properties used were log Kow of the neutral and anion species of the PFAS, and their polarizability. The model was specific enough to predict significantly different k values of unknown compounds with similar structures, which facilitated assignment of isomeric structures of PFAS.« less
4. Workflow for fast lipid tissue screening using LESA-FT-ICR-MS

   https://doi.org/10.1039/c8ay02739k  

   Haler, Jean R. N. ; Sisley, Emma K. ; Cintron-Diaz, Yarixa L. ; Meitei, Sanjib N. ; Cooper, Helen J. ; Fernandez-Lima, Francisco ( May 2019 , Analytical Methods)

   Lipid screening of biological substrates is an important step during biomarker detection and identification. In this work, a fast workflow is described capable of rapid screening for lipid components from biological tissues at ambient pressure based on liquid microjunction extraction in tandem with nano-electrospray ionization (nESI) with ultra-high resolution mass spectrometry, i.e. , liquid extraction surface analysis (LESA) coupled to Fourier-transform ion cyclotron resonance (tandem) mass spectrometry (LESA-FT-ICR-MS/MS). Lipid profiles are presented for thin tissue sections of mouse brain (MB) and liver (ML) samples, analyzed in both positive and negative mode by data-dependent acquisition (DDA) tandem FT-ICR-MS/MS. Candidate assignments were based on fragmentation patterns using mostly SimLipid software and accurate mass using mostly the LipidMaps database (average sub-ppm mass error). A typical, single point surface analysis (<1 mm spatial sampling resolution) lasted less than 15 minutes and resulted in the assignment of (unique and mulitple) lipid identifications of ∼190 (MB) and ∼590 (ML) m / z values. Despite the biological complexity, this led to unique identifications of distinct lipid molecules (sub-ppm mass error) from 38 different lipid classes, corresponding to 10–30% of the lipid m / z identifications.
5. Synthetic mimics of cyclic antimicrobial peptides via templated ring-opening metathesis (TROM)

   https://doi.org/10.1039/C9PY01271K  

   Zhou, Zhe ; Ergene, Cansu ; Palermo, Edmund F. ( January 2019 , Polymer Chemistry)

   We utilized a templated ring-opening metathesis (TROM) strategy to synthesize a series of precision macrocyclic olefins, each containing two, three or four repeating units of a cyclooctene with pendant carboxylic acid side chains. The structures were confirmed by a combination of NMR spectroscopy, MALDI, and MALDI ms/ms fragmentation studies. In accordance with previous work, we found that cyclooctene monomers covalently tethered to precision oligo(thiophene)s yield exclusively macrocyclic products when subjected to the Grubbs 3 rd generation catalyst in highly dilute solution (10 −4 M in DCM, 0 °C). Upon hydrolytic liberation of the daughter oligo(olefin) product, further derivatization with cationic groups confers antibacterial and hemolytic activities. We compare the biological activity of these precision macrocycles to that of a polydisperse sample prepared by direct ROM in the absence of a template. Surprisingly, the relatively ill-defined, disperse mixture of oligomeric species exerted biological activity comparable to that of the precision oligomeric macrocycles, suggesting a remarkable degree of tolerance for heterogeneity. These findings provide nuance to the structure–activity relationships understood thus far for AMPs and their mimics, especially in the context of relatively underexplored macrocyclic compounds.