Precursor Ion Research Articles

Highly sensitive ultra-performance liquid chromatography coupled with triple quadrupole mass spectrometry detection method for levoglucosan based on Na+ enhancing its ionization efficiency.

The sensitive determination of levoglucosan in aqueous samples has great significance for the study of biomass burning. Although some sensitive high-performance liquid chromatography/mass spectrometry (HPLC/MS) detection methods have been developed for levoglucosan, there are still plenty of shortcomings, such as complicated sample pre-treatment procedures, large-amount sample requirements, and poor reproducibility. Herein, a new method for the determination of levoglucosan in the aqueous sample was developed using ultra-performance liquid chromatography with triple quadrupole mass spectrometry (UPLC-MS/MS). In this method, we firstly found that compared with H+, Na+ could effectively enhance the ionization efficiency of levoglucosan, even though the content of H+ is higher in the environment. Moreover, the precursor ion m/z 185.1 [M + Na]+ could be used as a quantitative ion to sensitively detect levoglucosan in aqueous samples. Only 2 μL of un-pretreated sample is required for one injection in this method, and great linearity was obtained (R 2 = 0.9992) using the external standard method when the concentration of levoglucosan was 0.5-50 ng mL-1. The limit of detection (LOD) and quantification (LOQ) were 0.1 ng mL-1 (0.2 pg absolute mass injected) and 0.3 ng mL-1, respectively. Acceptable repeatability, reproducibility, and recovery were achieved. This method has the advantages of high sensitivity, good stability, good reproducibility, and simple operation, which could be widely used for the detection of different concentrations of levoglucosan in various water samples, especially for the detection of samples with low content such as ice core or snow samples.

Chemical constituents in different parts of Ixeris sonchifolia based on UPLC-LTQ-Orbitrap-MS~n

The chemical constituents in stem leaf, root, and flower of Ixeris sonchifolia were identified by the ultra performance li-quid chromatography coupled with linear ion trap quadrupole-orbitrap mass spectrometry(UPLC-LTQ-Orbitrap-MS~n). The separation was performed on an Acquity UPLC BEH C_(18) column(2.1 mm×100 mm, 1.7 μm) with a mobile phase of water(containing 0.1% formic acid, A)-acetonitrile(B) with gradient elution. With electrospray ionization source, the data of 70% methanol extract from stem leaf, root and flower of I. sonchifolia were collected by high-resolution full-scan Fourier transform spectroscopy, data dependent acquisition, precursor ion scan, and selected ion monitoring in the negative and positive ion modes. The compounds were identified based on accurate molecular weight, retention time, fragment ions, comparison with reference standard, Clog P and references. A total of 131 compounds were identified from the 70% methanol extract of I. sonchifolia, including nucleosides, flavonoids, organic acids, terpenoids, and phenylpropanoids, and 119, 110, and 126 compounds were identified from the stem leaf, root and flower of I. sonchifolia, respectively. In addition, isorhamnetin, isorhamnetin-7-O-sambubioside and caffeylshikimic acid were discovered from I. sonchifolia for the first time. This study comprehensively analyzed and compared the chemical constituents in different parts of I. sonchifolia, which facilitated the discovery of effective substances and the development and application of medicinal material resources of I. sonchifolia.

Characterization of ginsenoside structural isomers from mixtures using in situ methylation with direct analysis in real-time ionization tandem mass spectrometry

Characterization of structural isomers of bioactive molecules is important for recognizing their functions, but it has been challenging due to their highly similar structures. As the main bioactive constituents of Panax ginseng, ginsenosides have different structural isomers attributed to the aglycone structure and glycosylation sites as well as stereochemistry of sugar groups attached. This work demonstrated a simple and robust in situ methylation reaction with tetramethylammonium hydroxide (TMAH) using ambient ionization source of direct analysis in real time (DART) to characterize saponin structural isomers. The DART ion source provides favorable conditions to methylate hydroxyl groups of ginsenoside instantaneously with TMAH, and it can ionize the methylated products at the same time. Methylated ginsenoside stereoisomers even with subtle structure differences generated very different mass signals from full-scan MS and tandem MS. High-resolution mass spectrometry aided the assignment of molecular structures of the various precursor and fragment ions from different ginsenosides, which provided structural information for both the aglycone skeleton and the sugar moieties in ginsenosides. The presented method was successfully used for the identification of ginsenosides in Panax ginseng, and saponin isomers were characterized without the need for chromatographic separation and/or tedious offline sample pretreatment.

Analytical key issues and challenges in the LC-MS/MS determination of antibiotics in wastewater

The research on antibiotics occurrence in the aquatic environment has become a hot topic in the last years due to their potential negative effects, associated to possible bacterial antibiotic-resistance, after continuous exposure to these compounds. Most of antibiotic residues are not completely removed in the wastewater treatment plants (WWTPs) and end up in the aquatic environment through treated wastewater (WW). The development of reliable analytical methodologies for the determination of antibiotics in influent (IWW) and effluent wastewater (EWW) is needed with different purposes, among others: monitoring their occurrence in the aquatic environment, performing environmental risk assessment, estimating removal efficiencies of WWTPs, or estimating the consumption of these compounds. In this paper, we perform an in-depth investigation on analytical key issues that pose difficulties in the determination of antibiotics in complex matrices, such as WW, and we identify challenges to be properly addressed for successful analysis. The analytical technique selected was liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), as it is the most powerful and widely applied at present for antibiotic residues determination. The mass spectrometric behavior of 18 selected antibiotics, the chromatographic performance, ion ratio variations associated to the sample matrix when using different precursor ions or protomers, and the macrolides adsorption to glass vial, were some of the issues studied in this work. On the basis of the detailed study performed, an analytical LC-MS/MS method based on sample direct injection has been developed for quantification of 18 antibiotics in IWW and EWW, allowing their determination at low ng L−1 levels.

Differentiation of Isomeric, Nonseparable Carbohydrates Using Tandem-Trapped Ion Mobility Spectrometry-Mass Spectrometry.

Carbohydrates play important roles in biological processes, but their identification remains a significant analytical problem. While mass spectrometry has increasingly enabled the elucidation of carbohydrates, current approaches are limited in their abilities to differentiate isomeric carbohydrates when these are not separated prior to tandem-mass spectrometry analysis. This analytical challenge takes on increased relevance because of the pervasive presence of isomeric carbohydrates in biological systems. Here, we demonstrate that TIMS2-MS2 workflows enabled by tandem-trapped ion mobility spectrometry-mass spectrometry (tTIMS/MS) provide a general approach to differentiate isomeric, nonseparated carbohydrates. Our analysis shows that (1) cross sections measured by TIMS are sufficiently precise and robust for ion identification; (2) fragment ion cross sections from TIMS2 analysis can be analytically exploited to identify carbohydrate precursors even if the precursor ions are not separated by TIMS; (3) low-abundant fragment ions can be exploited to identify carbohydrate precursors even if the precursor ions are not separated by IMS. (4) MS2 analysis of fragment ions produced by TIMS2 can be used to validate and/or further characterize carbohydrate structures. Taken together, our analysis underlines the opportunities that tandem-ion mobility spectrometry/MS methods offer for the characterization of mixtures of isomeric carbohydrates.

Combining trapped ion mobility spectrometry with liquid chromatography and tandem mass spectrometry for analysis of isomeric PDE-5 inhibitor analogs

The detection and identification of phosphodiesterase type 5 enzyme (PDE-5) inhibitors in dietary supplements poses an analytical challenge due to the large number of analogs and isomers currently available and the continued introduction of novel analogs. The use of trapped ion mobility spectrometry (TIMS) in conjunction with liquid chromatography (LC) and electrospray ionization tandem mass spectrometry (MS/MS) was explored for the analysis of two groups of isomeric PDE-5 inhibitor analogs using a 5-minute method. Of the eight compounds studied, six were resolved by a combination of LC and TIMS; the two remaining isomers were distinguished by one or more unique product ions in the MS/MS spectrum. The results revealed that separation by LC corresponded to differences in substitution on the piperazine moiety of the PDE-5 inhibitors, while separation by TIMS corresponded to the position of a nitrogen atom in the fused ring region of the molecules. Samples prepared by spiking mixtures of varying amounts of the Group 2 isomers into a representative dietary supplement matrix were analyzed and concentrations determined from the mobility-adjusted extracted ion chromatograms exhibited relative standard deviations of 6.0 % or less for 17 of 20 measurements and recoveries between 80 % and 120 % for all measurements. Quantitative measurements from a short LC gradient were possible due to the reduced chemical background associated with the TIMS separation of co-eluting matrix compounds, which enabled acquisition of rapid and qualitatively relevant broadband collision induced dissociation spectra that didn’t require precursor ion isolation; the reduced chemical background permits non-targeted detection of novel analogs and eliminates the need for a separate method for quantitative measurement.

Complete Structural Elucidation of Monophosphorylated Lipid A by CID Fragmentation of Protonated Molecule and Singly Charged Sodiated Adducts.

Lipid A, the inflammatory portion of lipopolysaccharides (LPS, endotoxins), is the main component of the outer membrane of Gram-negative bacteria. Its bioactivity in humans and animals is strictly related to its chemical structure. In the present work, the fragmentation patterns of the singly charged monosodium [M + Na]+ and disodium [M - H + 2Na]+ adducts, as well as the protonated form of monophosphorylated lipid A species were investigated in detail using positive-ion electrospray ionization-based tandem (MS/MS) and multistage mass spectrometry (MSn) with low-energy collision-induced dissociation (CID). Several synthetic and native lipid A samples were included in the study. We found that the fragmentation pattern of disodiated lipid A is quite similar to that of the well-characterized deprotonated lipid A molecule (typically detected in the negative-ion mode), while the fragmentation pattern of monosodiated lipid A contains fragment ions similar to those of both protonated and deprotonated lipid A molecules. In summary, we propose a new mass spectrometry approach based on the fragmentation regularities of only positively charged precursor ions to dissect the location of the phosphate group and fatty acid moieties on monophosphorylated lipid A. Moreover, this study provides a better understanding of the so-called "chimera mass spectra", which are commonly detected during the fragmentation of native lipid A samples containing both C-1 and C-4' phosphate positional isomers but rarely identified in negative-ion mode.

Simulation of mass spectrometry-based proteomics data with Synthedia.

A large number of experimental and bioinformatic parameters must be set to identify and quantify peptides in mass spectrometry experiments and each of these will impact the results. An ability to simulate raw data with known contents would allow researchers to rapidly explore the effects of varying experimental parameters and systematically investigate downstream processing software. A range of data simulators are available for established data-dependent acquisition methodologies, but these do not extend to the rapidly developing field of data-independent acquisition (DIA) strategies. Here, we present Synthedia-a software package to simulate DIA liquid chromatography-mass spectrometry for bottom-up proteomics experiments. Synthedia can generate datasets with known peptide precursor ions and fragments and allows for the customization of a wide variety of chromatographic and mass spectrometry parameters. Synthedia is freely available via the internet and can be used through a graphical website (https://synthedia.org/) or locally via the command line (https://github.com/mgleeming/synthedia/). Supplementary data are available at Bioinformatics Advances online.

MS/MS molecular networking-guided in-depth profiling of triterpenoid saponins from the fruit of Eleutherococcus senticosus and their neuroprotectivity evaluation.

Eleutherococcus senticosus fruit (ESF) is a natural health supplement resource that has been extensively applied as a tonic for the nervous system. The structures and neural bioactivities of triterpenoid saponins (TS), which are the major constituents of ESF, have not been comprehensively analyzed thus far. We conducted a complete in-depth MS/MS molecular networking (MN)-based targeted analysis of TS from the crude extract of ESF and investigated its neuroprotective value. An MS/MS MN-guided strategy was used to rapidly present a series of precursor ions (PIs) of TS in a compound cluster as TS-targeted information used in the discovery and characterization of TS. In addition, a prepared TS-rich fraction of ESF was assayed for its restraining effects on β-amyloid-induced inhibition of neurite outgrowth. A total of 87 TS were discovered using a PI tracking strategy, 28 of which were characterized as potentially undescribed structures according to their high-resolution MS values. Furthermore, the TS-rich fraction can significantly reduce β-amyloid-induced damage to neural networks by promoting the outgrowth of neurites and axons. Our findings reveal the richness of TS in ESF and will accelerate their application in the treatment of neurodegenerative diseases.

Broken into pieces: The challenges of determining sulfonated azo dyes in biological reactor effluents using LC-ESI-MS/MS analysis

Most studies on the biodegradation of textile azo dyes use color as parameter for measuring the efficiency of degradation. Although widely employed, spectrophotometric methods are susceptible to the interference of metabolites or degradation products from the biological treatment. We propose a method for determination of a model sulfonated azo dye (Direct Black 22, DB22) in wastewater using solid-phase extraction (SPE) and liquid chromatography – electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). MS analysis in negative electrospray ionization mode showed DB22 as the most abundant precursor ion, corresponding to [M–3Na + H]2-, which yields two radical anions of m/z 370.1 and m/z 645 after MS/MS fragmentation by collision-induced dissociation (CID). Calibration curve presented adequate linearity and precision in the range of 120–1500 ng mL−1, and recovery and detection limit were appropriate to the typically employed working concentrations. Nevertheless, we observed that standard heating of DB22 under alkaline conditions to simulate the production of wastewater during dye-baths resulted in loss of MS/MS signal, without affecting color. Further analysis showed that DB22 undergoes hydrolysis and does not remain unaltered in solution. Alternative methods of hydrolysis evaluated resulted in no MS/MS signal as well. SPE-LC-ESI-MS/MS analysis evidenced the structural change of DB22 in aqueous solution while the dyeing-capacity was preserved. This technique has also the potential of being tailored to consider the detection of the hydrolyzed fragments of azo dyes in wastewater for appropriate quantification, but it was not the scope of the current step of this research. Color remains as a more reliable parameter for monitoring azo compounds which are unstable in aqueous solution, while a more robust and holistic method needs to be developed for the speciation of the DB22 products of thermal hydrolysis.

Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules.

In metabolomics studies using high-resolution mass spectrometry (MS), a set of product ion spectra is comprehensively acquired from observed ions using the data-dependent acquisition (DDA) mode of various tandem MS. However, especially for low-intensity signals, it is sometimes difficult to distinguish artifact signals from true fragment ions derived from a precursor ion. Inadequate precision in the measured m/z value is also one of the bottlenecks to narrowing down the candidate compositional formula. In this study, we report that averaging multiple product ion spectra can improve m/z precision as well as the reliability of fragment ions that are observed in such spectra. A graph-based method was applied to cluster a set of similar spectra from multiple DDA data files resulting in creating an averaged product-ion spectrum. The error levels for the m/z values declined following the central limit theorem, which allowed us to reduce the number of candidate compositional formulas. The improved reliability and precision of the averaged spectra will contribute to a more efficient annotation of product ion spectral data.

Energy release and product ion fragmentation in proton transfer reactions of N2H+ and ArH+ with acetone*

Proton transfer reaction mass spectrometry has a so far little exploited potential for the analysis of high-purity process and inert gases. In order to protonate impurities like saturated hydrocarbons, precursor ions with very low proton affinity must be used, which in turn leads to a large energy release upon protonation of molecules with high proton affinity, potentially causing fragmentation of the product ions. To explore the potential of low-proton affinity precursor ions like ArH+ and N2H+ for analytical purposes, we studied their gas-phase reactions and kinetics with acetone by Fourier transform ion cyclotron resonance (FT–ICR) mass spectrometry. The dominant product ion in both cases is protonated acetone, but fragment ions formed include C2H3O+, C3H5 + and CH3O+, which are formed in higher abundance with ArH+ compared to N2H+. The reaction efficiencies are determined to be close to 100%. Quantum chemical calculations reveal energetically favorable reaction pathways and explain the loss of water leading to the formation of C3H5 +, as well as loss of methane to yield C2H3O+ via dissociative proton attachment, which corresponds to the main product in the EI mass spectrum of acetone. Formation of protonated formaldehyde CH3O+ involves rearrangement of the C–C bonds to eliminate ethylene.

Synchronized Reverse Scan Collision Induced Dissociation in Digital Ion Trap Mass Spectrometer for Improving Fragment Ion Detection

Development of fragment ion detection methods is of great importance for mass spectrometer advancement or substance identification. To date, collision induced dissociation (CID) remains the most commonly used ion activation method in MS/MS experiments, and the effectiveness of CID in an ion trap mass spectrometer is limited by low mass cutoff and weak fragmentation yields. Theoretically, controlling the q value is the key to maintain the fragment efficiency and trapping efficiency of MS/MS, thus improving the detection of fragment ion, while currently reported techniques usually require complex circuitry and often produce different CID patterns. In this paper, with the developed synchronized reversed scanning-collision induced dissociation (SRS-CID) technique, we demonstrate its effective improvement in fragment ion detection. The SRS-CID is implemented on a digital ion trap mass spectrometer (DITMS) by reverse scanning the q values during CID process, or specifically, the frequency is increased during the CID process. With the SRS-CID technique, the fragmentation efficiency of precursor ions can be slightly improved. For reserpine analyte, the trapping efficiency for low-mass fragment ions is improved at least 3 times, and for YGGFL, the trapping efficiency for low-mass fragment ions is improved at least 9 times. These experimental results can also be validated by simulations, and the kinetic energy variation plot suggests consecutive fragmentation occurs. In any case, the SRS-CID provides a solution to the low efficiency of fragment ion detection during tandem MS analysis, which will certainly be useful in the future.

Characterization and identification of chemical constituents in Corni Fructus and effect of storage using UHPLC-LTQ-Orbitrap-MS

Corni Fructus (CF) has been widely used as both traditional medicine and food; however, systematic studies on its chemical profile and the impact of storage periods on the indicative components are lacking. In this study, UHPLC-LTQ-Orbitrap-MS was used to investigate the fragmentation behaviors of multiple compounds from CF and the content variety of its indicative components for different storage periods. The major basic components of CF were determined to be iridoid glucosides, pentacyclic triterpenoids, phenolic acids, tannins and flavonoids. The characteristic cleavage pathways of the iridoid glucosides, pentacyclic triterpenoids, phenolic acids, tannins and flavonoids were further investigated and elaborated, which could assist in identifying the structures of similar components of other Chinese herbal medicines. Using accurate mass measurements for each precursor ion and the subsequent fragmented ions, and then comparing with standards and literature data, a total of 130 components, including 69 iridoid glucosides, 9 pentacyclic triterpenoids, 16 phenolic acids, 20 tannins and 16 flavonoids, 47 of which are potentially new compounds, were identified. The storage period studies indicated that the contents of 19 indicative components in CF changed differently with the prolongation of the storage period. Among them, morroniside, loganin, sweroside, cornuside, gallic acid, oleanolic acid and ursolic acid were the most important. These results provide abundant information for the identification and improved understanding of the chemical constituents in CF to clarify the content variety of its indicative components for different storage periods.

Catalytic Dehydrogenation of Liquid Organic Hydrogen Carrier Model Compounds by CpM+ (M = Fe, Co, Ni) in the Gas Phase

Although there is much interest in developing liquid organic hydrogen carriers (LOHCs) and new metal catalysts to release hydrogen on demand for application in energy generation, few studies have provided mechanistic insights into the crucial metal-catalyzed dehydrogenation reactions. Here we use multistage mass spectrometry experiments and DFT calculations to examine the dehydrogenation of the LOHC model compounds cyclohexane, pyrrolidine, N-methylpyrrolidine, and piperidine by the half-sandwich cyclopentadienyl cations, [CpM]+ (M = Fe, Co, and Ni). The [CpM]+ ions were generated via collision-induced dissociation (CID) of precursor ions generated via electrospray ionization (ESI) of solutions of the compounds CpFe(CO)2I, Cp2Ni, and Cp2Co. The [CpFe]+ ion was found to catalyze triple dehydrogenation of cyclohexane to benzene via a combination of ion–molecule reactions (IMR) and CID experiments. Reactions of [CpM]+ (M = Co, Ni) were found to be more complex as dehydrogenation was accompanied by significant cyclohexane ring cleavage. Reactions of [CpFe]+ with the N-heterocyclic model compounds showed catalytic double dehydrogenation of pyrrolidine/N-methylpyrrolidine and triple dehydrogenation of piperidine. However, multiple side reactions were found, especially in the case of N-methylpyrrolidine and piperidine. They included proton transfer/hydride abstraction to/from the LOHC model methyl loss from the N-methylpyrrolidine complex, and NH2/NH3 extrusion from the piperidine complex. DFT calculations shed light on the structure of the key intermediates in all these systems.

Acetic Acid Ion Pairing Additive for Reversed-Phase HPLC Improves Detection Sensitivity in Bottom-up Proteomics Compared to Formic Acid.

Despite the general acceptance of formic acid as the additive of choice for peptide reversed-phase LC-MS/MS applications, some still argue that the selection of acetic acid represents a better option. To settle this debate, we investigated both the difference in MS sensitivity and chromatographic behavior of peptides between these two systems. This interlaboratory study was performed using different MS setups and C18 separation media employing both 0.1% formic and 0.5% acetic acid as ion pairing modifiers. Relative to formic acid, we find an overall ∼2.2-2.5× increase in MS signal and a slight decrease in RP LC retention (-0.7% acetonitrile on average) for acetic acid conditions. While these two features have opposing effects on peptide detectability, we find that acetic acid produces up to 60% higher peptide ID output depending on the type of sample. The drop in RPLC retention increases with peptide net charge at acidic pH. MS signal is dependent on the difference between the charge of the precursor ion and the charge of the peptide in solution, favoring species with a low pI. Lower peptide retention under acetic acid conditions demonstrates its higher hydrophilicity and, as expected, leads to composition and sequence-dependent character of the observed retention shift.

Efficient optimization and development of two methods for the determination of acrylamide in deep-frying oil by liquid chromatography-tandem mass spectrometry: Application of multifactor analysis assessment strategy.

A new multifactor analysis assessment strategy was developed for evaluating, optimizing, and comparing analytical techniques for acrylamide in frying oils. Based on five indices (absolute recovery, absolute matrix effect, the intensity of the full ion scan, and the precursor ion scan to m/z 184 and m/z 241), the proposed strategy was performed with radar analysis, relative contribution analysis, and the entropy-weighted technique for order performance by similarity to ideal solution analysis. Two novel methods based on quick, easy, cheap, effective, rugged, and safe extraction methodology and gel permeation chromatography-liquid-liquid extraction followed by liquid chromatography-tandem mass spectrometry have been developed for the analysis of acrylamide in frying oils. Two methods were suitable for rapid and sensitive analysis of acrylamide in oils in different laboratories, with a limit of quantitation at 2μg/kg, and the average recovery ranging from 92.5% to 107.8%, with relative standard deviations below 10%. When considering automation efficiency and matrix effects, gel permeation chromatography is the most efficient method, whereas the other method has an advantage when analyzing large samples. The developedmethods were used in a pilot study to analyze frying oils with acrylamide content below 9.82μg/kg, showing that the repeated frying process did not produce significant content of acrylamide in oils.

A Comprehensive Study on the Chemical Constituents and Pharmacokinetics of Erzhi Formula and Jiawei Erzhi Formula Based on Targeted and Untargeted LC-MS Analysis.

Erzhi formula (EZF) is a traditional Chinese medicine prescription, which has been widely used in the treatment of osteoporosis and premature ovarian failure. To enhance curative effects, the other two herbal medicines, including Spatholobi Caulis (SC) and Achyranthes bidentata Blume (ABB), were added into the original EZF formula to obtain two new Jiawei-EZF (JW-EZF) preparations. To clarify the effect of the compatibility of herbs for original formulas, the chemical constituents and bioactive compounds in vivo were detected. An efficient and sensitive targeted and untargeted UHPLC/ESI-Q-Orbitrap MS method, together with mass defect filter and precursor ion list, was established firstly for the profiling of different EZF formulas. Furthermore, eleven absorbed compounds (apigenin, luteoloside, luteolin, oleuropein, wedelolactone, acteoside, specnuezhenide, 11-methyloleoside, ecliptasaponin A, formononetin, and β-ecdysone) were simultaneously quantified in rat plasma. A total of 124, 162, and 177 compounds were identified or tentatively identified in EZF, JW-3-EZF (EZF+SC) and JW-4-EZF (EZF+SC+ABB), respectively. 110 compounds were found to be common constituents in the three formulas. Moreover, 66 prototypes were unambiguously identified in the rats' plasma after oral administration of the three formulas using the same strategy. 11 out of the 66 absorbed components were simultaneously quantitated in the pharmacokinetic (PK) study. Compared to the original EZF, the plasma AUC(0-24h) and AUC(0-∞) of apigenin, 11-methyloleoside, luteolin, luteoloside, wedelolactone, and acteoside were found to be significantly increased after oral administration of JW-3-EZF, and plasma AUC(0-24h) and AUC(0-∞) of apigenin, wedelolactone, and acteoside, were also found to be significantly increased after JW-4-EZF administration. The combined qualitative and quantitative methods were used to provide a potential approach to the characterization and quality control of the Traditional Chinese Medicine (TCM) and its preparations.

A de novo MS1 feature detector for the Bruker timsTOF Pro.

Identification of peptides by analysis of data acquired by the two established methods for bottom-up proteomics, DDA and DIA, relies heavily on the fragment spectra. In DDA, peptide features detected in mass spectrometry data are identified by matching their fragment spectra with a peptide database. In DIA, a peptide's fragment spectra are targeted for extraction and matched with observed spectra. Although fragment ion matching is a central aspect in most peptide identification strategies, the precursor ion in the MS1 data reveals important characteristics as well, including charge state, intensity, monoisotopic m/z, and apex in retention time. Most importantly, the precursor's mass is essential in determining the potential chemical modification state of the underlying peptide sequence. In the timsTOF, with its additional dimension of collisional cross-section, the data representing the precursor ion also reveals the peptide's peak in ion mobility. However, the availability of tools to survey precursor ions with a wide range of abundance in timsTOF data across the full mass range is very limited. Here we present a de novo feature detector called three-dimensional intensity descent (3DID). 3DID can detect and extract peptide features down to a configurable intensity level, and finds many more features than several existing tools. 3DID is written in Python and is freely available with an open-source MIT license to facilitate experimentation and further improvement (DOI 10.5281/zenodo.6513126). The dataset used for validation of the algorithm is publicly available (ProteomeXchange identifier PXD030706).

Quantification of Paeoniflorin by Fully Validated LC-MS/MS Method: Its Application to Pharmacokinetic Interaction between Paeoniflorin and Verapamil.

A rapid, sensitive, and specific LC-MS/MS method was developed and fully validated for the detection of paeoniflorin only in rat plasma, and applied to pharmacokinetic studies, including intravenous, multi-dose oral and combined administrations with verapamil. In this study, tolbutamide was used as the internal standard, and the protein precipitation extraction method, using acetonitrile as the extraction agent, was used for the sample preparation. Subsequently, the supernatant samples were analyzed on a Phenomenex Gemini® NX-C18 column with a flow rate of 1.0 mL/min in a gradient elution procedure. In the extracted rat plasma, the method exhibited high sensitivity (LLOQ of 1.0 ng/mL) upon selecting ammonium adduct ions ([M+NH4]+) as the precursor ions and good linearity over the concentration range of 1.0−2000 ng/mL, with correlation coefficients >0.99. The intra- and inter-batch accuracy RE% values were within ±8.2%, and the precision RSD% values were ≤8.1% and ≤10.0%, respectively. The results show that the method can be successfully applied to quantitate paeoniflorin in biological samples. Additionally, paeoniflorin is subsequently confirmed to be the substrate of the P-gp transporter in vivo and in vitro for the first time, which would be necessary and beneficial to investigate the clinical safety and efficacy of PF with other drugs in the treatment of rheumatoid arthritis.