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1. Development of a relative quantification method for infrared matrix‐assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings

   https://doi.org/10.1002/rcm.8616  

   Bagley, M_Caleb; Stepanova, Anna_N; Ekelöf, Måns; Alonso, Jose_M; Muddiman, David_C (February 2020, Rapid Communications in Mass Spectrometry)

   RationaleMass spectrometry imaging of young seedlings is an invaluable tool in understanding how mutations affect metabolite accumulation in plant development. However, due to numerous biological considerations, established methods for the relative quantification of analytes using infrared matrix‐assisted laser desorption electrospray ionization (IR‐MALDESI) mass spectrometry imaging are not viable options. In this study, we report a method for the quantification of auxin‐related compounds using stable‐isotope‐labelled (SIL) indole‐3‐acetic acid (IAA) doped into agarose substrate. MethodsWild‐typeArabidopsis thalianaseedlings,sur2andwei8 tar2loss‐of‐function mutants, andYUC1gain‐of‐function line were grown for 3 days in the dark in standard growth medium. SIL‐IAA was doped into a 1% low‐melting‐point agarose gel and seedlings were gently laid on top for IR‐MALDESI imaging with Orbitrap mass spectrometry analysis. Relative quantification was performed post‐acquisition by normalization of auxin‐related compounds to SIL‐IAA in the agarose. Amounts of auxin‐related compounds were compared between genotypes to distinguish the effects of the mutations on the accumulation of indolic metabolites of interest. ResultsIAA added to agarose was found to remain stable, with repeatability and abundance features of IAA comparable with those of other compounds used in other methods for relative quantification in IR‐MALDESI analyses. Indole‐3‐acetaldoxime was increased insur2mutants compared with wild‐type and other mutants. Other auxin‐related metabolites were either below the limits of quantification or successfully quantified but showing little difference among mutants. ConclusionsAgarose was shown to be an appropriate sampling surface for IR‐MALDESI mass spectrometry imaging ofArabidopsisseedlings. SIL‐IAA doping of agarose was demonstrated as a viable technique for relative quantification of metabolites in live seedlings or tissues with similar biological considerations. 

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2. Comparison of δ ¹³ C analyses of individual foraminifer ( Orbulina universa ) shells by secondary ion mass spectrometry and gas source mass spectrometry

   https://doi.org/10.1002/rcm.9658  

   Wycech, Jody_B; Kelly, Daniel_Clay; Kozdon, Reinhard; Ishida, Akizumi; Kitajima, Kouki; Spero, Howard_J; Valley, John_W (November 2023, Rapid Communications in Mass Spectrometry)

   Abstract RationaleThe use of secondary ion mass spectrometry (SIMS) to perform micrometer‐scalein situcarbon isotope (δ¹³C) analyses of shells of marine microfossils called planktic foraminifers holds promise to explore calcification and ecological processes. The potential of this technique, however, cannot be realized without comparison to traditional whole‐shell δ¹³C values measured by gas source mass spectrometry (GSMS). MethodsPaired SIMS and GSMS δ¹³C values measured from final chamber fragments of the same shell of the planktic foraminiferOrbulina universaare compared. The SIMS–GSMS δ¹³C differences (Δ¹³C_SIMS‐GSMS) were determined via paired analysis of hydrogen peroxide‐cleaned fragments of modern cultured specimens and of fossil specimens from deep‐sea sediments that were either untreated, sonicated, and cleaned with hydrogen peroxide or vacuum roasted. After treatment, fragments were analyzed by a CAMECA IMS 1280 SIMS instrument and either a ThermoScientific MAT‐253 or a Fisons Optima isotope ratio mass spectrometer (GSMS). ResultsPaired analyses of cleaned fragments of cultured specimens (n = 7) yield no SIMS–GSMS δ¹³C difference. However, paired analyses of untreated (n = 18) and cleaned (n = 12) fragments of fossil shells yield average Δ¹³C_SIMS‐GSMSvalues of 0.8‰ and 0.6‰ (±0.2‰, 2 SE), respectively, while vacuum roasting of fossil shell fragments (n = 11) removes the SIMS–GSMS δ¹³C difference. ConclusionsThe noted Δ¹³C_SIMS‐GSMSvalues are most likely due to matrix effects causing sample–standard mismatch for SIMS analyses but may also be a combination of other factors such as SIMS measurement of chemically bound water. The volume of material analyzed via SIMS is ~10⁵times smaller than that analyzed by GSMS; hence, the extent to which these Δ¹³C_SIMS‐GSMSvalues represent differences in analyte or instrument factors remains unclear. 

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3. Machine Learning in Small-Molecule Mass Spectrometry

   https://doi.org/10.1146/annurev-anchem-071224-082157  

   Hong, Yuhui; Ye, Yuzhen; Tang, Haixu (May 2025, Annual Review of Analytical Chemistry)

   Tandem mass spectrometry (MS/MS) is crucial for small-molecule analysis; however, traditional computational methods are limited by incomplete reference libraries and complex data processing. Machine learning (ML) is transforming small-molecule mass spectrometry in three key directions: (a) predicting MS/MS spectra and related physicochemical properties to expand reference libraries, (b) improving spectral matching through automated pattern extraction, and (c) predicting molecular structures of compounds directly from their MS/MS spectra. We review ML approaches for molecular representations [descriptors, simplified molecular-input line-entry (SMILE) strings, and graphs] and MS/MS spectra representations (using binned vectors and peak lists) along with recent advances in spectra prediction, retention time, collision cross sections, and spectral matching. Finally, we discuss ML-integrated workflows for chemical formula identification. By addressing the limitations of current methods for compound identification, these ML approaches can greatly enhance the understanding of biological processes and the development of diagnostic and therapeutic tools. 

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4. Ion mobility–tandem mass spectrometry of bulky tert ‐butyl thiol ligated gold nanoparticles

   https://doi.org/10.1002/jms.4998  

   Wijesinghe, Kalpani_H; Hood, Christopher; Mattern, Daniell; Angel, Laurence_A; Dass, Amala (January 2024, Journal of Mass Spectrometry)

   Abstract Gold nanoparticles (AuNPs) synthesized in the 1–3 nm range have a specific number of gold core atoms and outer protecting ligands. They have become one of the “hot topics” in recent decades because of their interesting physical and chemical properties. The characterization of their structures is usually achieved by crystal X‐ray diffraction although the structures of some AuNPs remain unknown because they have not been successfully crystallized. An alternative method for studying the structure of AuNPs is electrospray ionization–ion mobility–tandem mass spectrometry (ESI‐IM‐MSMS). This research evaluated how effectively ESI‐IM‐MSMS using the commercially available Waters Synapt XS instrument yielded useful structural information from two AuNPs; Au₂₃(S‐tBu)₁₆and Au₃₀(S‐tBu)₁₈. The study used the maximum range of available collision energies along with ion mobility separation to measure the energy‐dependence of the product ions and their drift times which is a measure of their spatial size. For Au₂₃(S‐tBu)₁₆, the dissociation gave the masses of the outer protecting monomeric [RS–Au–SR] and trimeric [SR–Au–SR–Au–SR–Au–SR] staples where R = tBu, and complete dissociation of the outer layer Au andtBu groups to reveal the Au₁₅S₈core. For Au₃₀(S‐tBu)₁₈, the dissociation products was primarily through the loss of the partial ligands S‐tBu andtBu from the outer protecting layer and the loss of single Au₄(S‐tBu)₄unit. These results showed the that ESI‐IM‐MSMS analysis of the smaller Au₂₃(S‐tBu)₁₆gave information on all it major structural components whereas for Au₃₀(S‐tBu)₁₈, the overall structural information was limited to the ligands of the outer layer. 

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5. Tandem‐trapped ion mobility spectrometry/mass spectrometry coupled with ultraviolet photodissociation

   https://doi.org/10.1002/rcm.9192  

   Liu, Fanny_C; Ridgeway, Mark_E; Winfred, J_S_Raaj_Vellore; Polfer, Nicolas_C; Lee, Jusung; Theisen, Alina; Wootton, Christopher_A; Park, Melvin_A; Bleiholder, Christian (September 2021, Rapid Communications in Mass Spectrometry)

   RationaleTandem‐ion mobility spectrometry/mass spectrometry methods have recently gained traction for the structural characterization of proteins and protein complexes. However, ion activation techniques currently coupled with tandem‐ion mobility spectrometry/mass spectrometry methods are limited in their ability to characterize structures of proteins and protein complexes. MethodsHere, we describe the coupling of the separation capabilities of tandem‐trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS) with the dissociation capabilities of ultraviolet photodissociation (UVPD) for protein structure analysis. ResultsWe establish the feasibility of dissociating intact proteins by UV irradiation at 213 nm between the two TIMS devices in tTIMS/MS and at pressure conditions compatible with ion mobility spectrometry (2–3 mbar). We validate that the fragments produced by UVPD under these conditions result from a radical‐based mechanism in accordance with prior literature on UVPD. The data suggest stabilization of fragment ions produced from UVPD by collisional cooling due to the elevated pressures used here (“UVnoD2”), which otherwise do not survive to detection. The data account for a sequence coverage for the protein ubiquitin comparable to recent reports, demonstrating the analytical utility of our instrument in mobility‐separating fragment ions produced from UVPD. ConclusionsThe data demonstrate that UVPD carried out at elevated pressures of 2–3 mbar yields extensive fragment ions rich in information about the protein and that their exhaustive analysis requires IMS separation post‐UVPD. Therefore, because UVPD and tTIMS/MS each have been shown to be valuable techniques on their own merit in proteomics, our contribution here underscores the potential of combining tTIMS/MS with UVPD for structural proteomics. 

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