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1. Methods of Metabolite Identification Using MS/MS Data

   https://doi.org/10.1080/08874417.2019.1681328  

   Kwak, Myungjae; Kang, Kyungwoo; Wang, Yingfeng (January 2022, Journal of Computer Information Systems)
2. NanoSF-MS

   Mahmoud Elhusseiny Mostafa, James P. (September 2022, Journal of the American Society for Mass Spectrometry)

   Supercritical fluids are typically electrosprayed using an organic solvent makeup flow to facilitate continuous electrical connection and enhancement of electrospray stability. This results in sample dilution, loss in sensitivity, and potential phase separation. Premixing the supercritical fluid with organic solvent has shown substantial benefits to electrospray efficiency and increased analyte charge state. Presented here is a nanospray mass spectrometry system for supercritical fluids (nSF-MS). This split flow system used small i.d. capillaries, heated interface, inline frit, and submicron emitter tips to electrospray quaternary alkyl amines solvated in supercritical CO2 with a 10% methanol modifier. Analyte signal response was evaluated as a function of total system flow rate (0.5–1.5 mL/min) that is split to nanospray a supercritical fluid with linear flow rates between 0.07 and 0.42 cm/sec and pressure ranges (15–25 MPa). The nSF system showed mass-sensitive detection based on increased signal intensity for increasing capillary i.d. and analyte injection volume. These effects indicate efficient solvent evaporation for the analysis of quaternary amines. Carrier additives generally decreased signal intensity. Comparison of the nSF-MS system to the conventional SF makeup flow ESI showed 10-fold signal intensity enhancement across all the capillary i.d.s. The nSF-MS system likely achieves rapid solvent evaporation of the SF at the emitter point. The developed system combined the benefits of the nanoemitters, sCO2, and the low modifier percentage which gave rise to enhancement in MS detection sensitivity. 

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3. U-Pb dating of accessory minerals by LA-ICP-MS/MS

   Stone, JS; Cruz-Uribe, AM; Brooks, HL; Walters, J (January 2019, 2019 Fall Meeting AGU)

   Titanite and apatite can incorporate significant amounts of common Pb (204Pb) into their mineral structures, which leads to uncertainty when applying the U-Pb decay series for geochronology. The isobaric interference between 204Pb and 204Hg creates an additional complexity when calculating common lead corrections. Here we investigate the removal of 204Hg interferences during titanite U-Pb dating using reaction cell gas chemistry via triple quadrupole mass spectrometry compared with traditional methods that calculate U-Pb ages using a common lead correction. U-Pb dates for titanite natural reference materials MKED-1 and BLR-1 were determined using an ESI NWR193UC excimer laser coupled with an Agilent 8900 ‘triple quadrupole’ mass spectrometer. The 8900 is equipped with an octopole collision/reaction cell, which enables online interference removal. In order to compare traditional methods for U-Pb dating with interference removal methods, two experiments were run, one in which data was collected in NoGas mode, and one in which the 8900 was run in MS/MS mode, in order to assess the feasibility of determining U/Pb ratios with mass shifted isotopes. In MS/MS mode, NH3 was flowed through the reaction cell in order to enable a charge transfer reaction between NH3 and Hg+, effectively neutralizing Hg. During spot analyses in NoGas mode, masses 202Hg, 204Hg, 204Pb, 206Pb, 207Pb, 208Pb, 232Th, 235U, and 238U were monitored. For spot analyses in MS/MS mode, Th and U isotopes were measured on-mass at 232Th, 235U, 238U and mass-shifted to 247Th, 250U, and 253U. Pb isotopes were measured on-mass since Pb does not react with NH3. Ratios for 207Pb/235U, 206Pb/238U, and 207Pb/206Pb were calculated in Iolite (v.3.7.1) using the Geochron4 DRS using MKED-1 as the primary reference material and BLR-1 as a secondary reference material. Dates were calculated using IsoplotR. Weighted mean ages for titanite BLR-1 in MS/MS mode are 1043.8 ± 10.5 Ma (2σ, MSWD=1.08) for U isotopes measured on mass, and 1039.7 ± 8.3 Ma (2σ, MSWD=1.08) for mass-shifted U isotopes. These dates are both in agreement with the TIMS 206Pb/238U date for the BLR-1 titanite of 1047.1 ± 0.4 Ma. The use of NH3 for reaction cell chemistry has the potential to enable measurement of 204Pb without needing to correct for Hg interferences. 

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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. Direct sequencing of total S. cerevisiae tRNAs by LC-MS/MS

   https://doi.org/10.1261/rna.079656.123  

   Jones, Joshua D; Simcox, Kaley M; Kennedy, Robert T; Koutmou, Kristin S (May 2023, RNA)

   Among RNAs, transfer RNAs (tRNAs) contain the widest variety of abundant post-transcriptional chemical modifications. These modifications are crucial for tRNAs to participate in protein synthesis, promoting proper tRNA structure and aminoacylation, facilitating anticodon:codon recognition, and ensuring the reading frame maintenance of the ribosome. While tRNA modifications were long thought to be stoichiometric, it is becoming increasingly apparent that these modifications can change dynamically in response to the cellular environment. The ability to broadly characterize the fluctuating tRNA modification landscape will be essential for establishing the molecular level contributions of individual sites of tRNA modification. The locations of modifications within individual tRNA sequences can be mapped using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). In this approach, a single tRNA species is purified, treated with ribonucleases and the resulting single-stranded RNA products are subject to LC-MS/MS analysis. The application of LC-MS/MS to study tRNAs is limited by the necessity of analyzing one tRNA at a time because the digestion of total tRNA mixtures by commercially available ribonucleases produces many short digestion products unable to be uniquely mapped back to a single site within a tRNA. We overcame these limitations by taking advantage of the highly structured nature of tRNAs to prevent the full digestion by single-stranded RNA specific ribonucleases. Folding total tRNA prior to digestion allowed us to sequence S. cerevisiae tRNAs with up to 97% sequence coverage for individual tRNA species by LC-MS/MS. This method presents a robust avenue for directly detecting the distribution of modifications in total tRNAs. 

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