High-Precision, Gas-Phase Hydrogen/Deuterium-Exchange Kinetics by Mass Spectrometry Enabled by Exchange Standards.

Mass spectrometry (MS) has become a primary tool for identifying and quantifying biological molecules. In combination with other orthogonal techniques, such as gas-phase hydrogen/deuterium exchange (gHDX), MS is also capable of probing the structure of ions. However, gHDX kinetics can depend strongly on many factors, including laboratory temperature, instrumental conditions, and instrument platform selection. These effects can lead to high variability with gHDX measurements, which has hindered the broader adoption of gHDX for structural MS. Here we introduce an approach for standardizing gHDX measurements using cosampled standards. Quantifying the exchange kinetics for analytes relative to the exchange kinetics of the standards results in greater accuracy and precision than the underlying absolute measurements. The standardization was found to be effective for several types of analytes including small molecules and intact proteins. A subset of analytes showed deviations in their standardized exchange profiles that are attributed to field heating and the concomitant conformational isomerization. Inclusion of helium during the gHDX process for collisional cooling helps mitigate such variations in exchange kinetics related to ion heating. We anticipate that the outcomes of this research will enable the broader use of gHDX in MS-based workflows for molecular identification and isomer differentiation.

Determination of trans-resveratrol and its metabolites in rat serum using liquid chromatography with high-resolution time of flight mass spectrometry.

In this study we developed a sensitive method using high performance liquid chromatography (HPLC) coupled to electrospray ionization (ESI) with high resolution time of flight (TOF) mass spectrometry (MS) for the determination of naturally occurring antioxidant trans-resveratrol (3,5,4'-trihydroxy-trans-stilbene, RES). This method enabled an investigation of a relationship between tumor growth in rats and concentration of RES and its primary metabolites, trans-resveratrol-3-O-sulfate-3-O-sulfate (R3S) and trans-resveratrol-3-O-ß-d-glucuronide (R3G), in rat serum after RES exposure (5 or 25mg/kg/day). RES levels in rat serum were near the limit of detection, showing concentrations of 4±1 and 12±4ng/mL for low and high-dose exposure, respectively. Compared to RES, higher concentrations were found for its metabolites (R3G:4.8±0.3 and 6.8±0.3µg/mL; R3S:0.27±0.09 and 0.34±0.04µg/mL, respectively). Using TOF, for the first time, we measured the matrix affected limits of detection (LODs) in plasma (3.7, 82.4, and 4.7ng/mL for RES, R3G, and R3S, respectively), which were comparable to those reported in previous work using HPLC tandem mass spectrometry, but with a benefit of a full mass spectral profile. The ability to acquire data in full scan mode also revealed other isomers of R3S. The additional novelty of our study is in synthesis and application of deuterated recovery standards enabling accurate and precise quantification. In order to develop a robust method, the ESI conditions were optimized using a multilevel full factorial design of experiments.

Toward standardizing deuterium content reporting in hydrogen exchange-MS.

We introduce a method to monitor dispensing ratios during labeling reactions in hydrogen exchange (HX)-MS. The method corrects for systematic and random dispensing errors and harmonizes data incorporating variable %D2O in the experiment design. A correction factor for deuterium levels is obtained by quantifying the relative signal intensities arising from nonexchanging heavy caffeine (spiked into labeling buffer) and light caffeine (spiked into sample solutions). Dispensing variability over a wide range of %D2O composition can be detected and corrected to a common value, and although random dispensing error is usually minor, we show it can be the limiting factor in high quality signal measurements. Applying a dispensing control is therefore an effective tool for monitoring measurement precision in HX-MS.

Resolving isotopic fine structure to detect and quantify natural abundance- and hydrogen/deuterium exchange-derived isotopomers.

Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) is used for analyzing protein dynamics, protein folding/unfolding, and molecular interactions. Until this study, HDX MS experiments employed mass spectral resolving powers that afforded only one peak per nominal mass in a given peptide's isotope distribution, and HDX MS data analysis methods were developed accordingly. A level of complexity that is inherent to HDX MS remained unaddressed, namely, various combinations of natural abundance heavy isotopes and exchanged deuterium shared the same nominal mass and overlapped at previous resolving powers. For example, an A + 2 peak is comprised of (among other isotopomers) a two-(2)H-exchanged/zero-(13)C isotopomer, a one-(2)H-exchanged/one-(13)C isotopomer, and a zero-(2)H-exchanged/two-(13)C isotopomer. Notably, such isotopomers differ slightly in mass as a result of the ∼3 mDa mass defect between (2)H and (13)C atoms. Previous HDX MS methods did not resolve these isotopomers, requiring a natural-abundance-only (before HDX or "time zero") spectrum and data processing to remove its contribution. It is demonstrated here that high-resolution mass spectrometry can be used to detect isotopic fine structure, such as in the A + 2 profile example above, deconvolving the isotopomer species resulting from deuterium incorporation. Resolving isotopic fine structure during HDX MS therefore permits direct monitoring of HDX, which can be calculated as the sum of the fractional peak magnitudes of the deuterium-exchanged isotopomers. This obviates both the need for a time zero spectrum as well as data processing to account for natural abundance heavy isotopes, saving instrument and analysis time.

Separation and identification of degradation products in eprinomectin formulation using LC, LTQ FT-MS, H/D exchange, and NMR.

The aim of this study was to evaluate the suitability of the compendial active pharmaceutical ingredient (API) method for the analysis of finished products and characterization of degradation products in eprinomectin (EPM) samples. Heat stressed sample tests revealed a limitation of the API method in distinguishing an impurity merging with the principal analyte peak. A new selective, specific and sensitive method was therefore developed for the determination of EPM in formulations that separates its degradation products currently undetectable with the official method. The determination was carried out by reversed-phase HPLC using an isocratic solvent elution. The method was validated and found to be precise, accurate and specific; the detector response was linear over 50-150 µg/ml (EPM) and 0.1-3 µg/ml (degradation product) range of concentrations. Two major degradation products detected with the new method were isolated from sample matrices and characterized using LC-PDA, high resolution FT-ICR MS, NMR and hydrogen/deuterium exchange (HX-MS) studies. FTMS analysis showed accurate mass of molecular ion peaks for EPM and its two degradation products at m/z 914.52505 (mass error ≤ 1 ppm) with almost identical fragmentation patterns. Given the isomeric nature of the compounds, all three were further evaluated by ¹H, ¹³C, 1D NOESY and 2D (COSY) NMR experiments. The interpretation of experimental data positively identified Unknown 1 as the 2-epimer of EPM and Unknown 2 as the structural isomer Δ2,3-EPM containing a conjugated enoate. The new HPLC method and identification exercise is useful for analysis of EPM and its degradation products.

Normal carbon acid referencing for protein amide hydrogen exchange.

Measurement of the exchange kinetics for amide hydrogens along the protein backbone continues to offer valuable insights into structural stability and conformational dynamics. Since such studies routinely compare samples that differ in solution conditions or mechanical handling, normalization of the relative exchange rates can present a potentially significant source of experimental uncertainty. The carbon acids 1,3-dimethylimidazolium cation and thiomethylacetonitrile exhibit base catalyzed exchange rates similar to those of the slowly exchanging amides, under conditions typical for protein studies. With 13C enrichment at the acidic carbon position to facilitate selective observation, such carbon acids offer practical internal calibration of exchange.

Extensive deuterium back-exchange in certain immobilized pepsin columns used for H/D exchange mass spectrometry.

Pepsin digestion prior to mass analysis increases the spatial resolution of hydrogen exchange mass spectrometry experiments. Online digestion with immobilized pepsin is advantageous for several reasons including better digestion efficiency. We have found that certain immobilized pepsin columns cause substantial deuterium back-exchange, rendering the data unusable. When pepsin immobilized on a POROS support was used for online digestion, back-exchange was within the expected range and was similar to the back-exchange of deuterated peptides produced by in-solution pepsin digestion. However, when pepsin immobilized onto selected polystyrene-divinylbenzene supports was used for online digestion with the same system, deuterium loss was extremely high. The effect seems linked to the properties of the solid support used to conjugate the pepsin.