MS Experiments Research Articles

A Novel Bi2O3 Modified C-doped Hollow TiO2 Sphere Based on Glucose-derived Carbon Sphere with Enhanced Visible Light Photocatalytic Activity

The hydrothermal method was used to synthesize carbon sphere, and the hard template synthesis method was used to prepared C-doped hollow TiO2 sphere (CHTS). Bismuth nitrate was used as bismuth source to modify CHTS. The composite material was oxidized in air atmosphere at 450℃ to obtain Bi2O3 modified C-doped TiO2 hollow spheres(BCHTS). The morphology, elemental composition and photocatalytic degradation efficiency of tetracyclines (TC) by BCHTS hollow spheres were characterized by various measurements. Additionally, the possible transformation pathways and degradation mechanism of tetracycline were revealed via LC–MS and trapping experiments. The experimental results show that the Bi nanoparticles are uniformly dispersed in the CHTS. The photocatalyst exhibits enhanced degradation rate of TC (98.4% under visible-light within 180 min and 99.4% under natural light within 50 min) for its structure and narrow bandgap (2.87 eV). After five degradation cycles, the photocatalyst still remains high removal rate of 96.4% for TC. The results indicate that the photocatalyst may be promising for degrading antibiotic residuals remains. According to the trapping experiment, OH and h+ have a certain role on the photodegradation process, while·O2− is the main active species for degrading TC.

Automated Annotation of Untargeted All-Ion Fragmentation LC-MS Metabolomics Data with MetaboAnnotatoR.

Untargeted metabolomics and lipidomics LC–MS experiments produce complex datasets, usually containing tens of thousands of features from thousands of metabolites whose annotation requires additional MS/MS experiments and expert knowledge. All-ion fragmentation (AIF) LC–MS/MS acquisition provides fragmentation data at no additional experimental time cost. However, analysis of such datasets requires reconstruction of parent–fragment relationships and annotation of the resulting pseudo-MS/MS spectra. Here, we propose a novel approach for automated annotation of isotopologues, adducts, and in-source fragments from AIF LC–MS datasets by combining correlation-based parent–fragment linking with molecular fragment matching. Our workflow focuses on a subset of features rather than trying to annotate the full dataset, saving time and simplifying the process. We demonstrate the workflow in three human serum datasets containing 599 features manually annotated by experts. Precision and recall values of 82–92% and 82–85%, respectively, were obtained for features found in the highest-rank scores (1–5). These results equal or outperform those obtained using MS-DIAL software, the current state of the art for AIF data annotation. Further validation for other biological matrices and different instrument types showed variable precision (60–89%) and recall (10–88%) particularly for datasets dominated by nonlipid metabolites. The workflow is freely available as an open-source R package, MetaboAnnotatoR, together with the fragment libraries from Github (https://github.com/gggraca/MetaboAnnotatoR).

Radical fragment ions in collision-induced dissociation-based tandem mass spectrometry

Collision-induced dissociation (CID) is a common fragmentation strategy in tandem mass spectrometry (MS2) analysis. A conventional understanding is that fragment ions generated in low-energy CID should follow the even-electron rule. As such, (de)protonated ([M+H]+/[M−H]−) or even-electron precursor ions should follow heterolytic cleavages and predominately generate even-electron fragment ions with very few radical fragment ions (RFIs). However, the extent to which RFIs present in MS2 spectra has not been comprehensively investigated. This work uses the annotated high-resolution MS2 spectra from the latest NIST 20 tandem mass spectral library to investigate the occurrence of RFIs in CID MS2 experiments. In particular, RFIs were recognized using integer double bond equivalent (DBE) values calculated from their annotated molecular formulas. Our study shows that 65.4% and 68.8% of MS2 spectra of even-electron precursors contain at least 10% RFIs by ion-count (total number of ions) in positive and negative electrospray ionization modes, respectively. Furthermore, we classified chemicals based on their compound classes and chemical substructures, and calculated the percentages of RFIs in each class. As expected, compounds that can stabilize the radical site via resonance, such as aromatic and conjugated double bond-containing chemicals, are more likely to form RFIs. We also found four possible patterns of change in RFI percentages as a function of CID collision energy. Finally, we demonstrate that the inadequate consideration of RFIs in most conventional bioinformatic tools might be problematic during in silico fragmentation and de novo annotation of MS2 spectra. This work provides a further understanding of CID MS2 mechanisms, and the unexpectedly large percentage of RFIs suggests that the even-electron rule seems to be challenged in numerous cases where it is disobeyed.

Infrared Photoactivation Boosts Reporter Ion Yield in Isobaric Tagging.

Isobaric tagging facilitates multiplexed experiments that can determine sequences and relative amounts of peptides in biological samples using tandem mass spectrometry (MSn). Limited reporter ion generation limits quantitative accuracy and precision. As reporter ions are susceptible to unintended fragmentation and scattering by high-energy collisions, we activated peptides with IR photons and prevented successive dissociation of generated reporter ions with ion parking, which altogether boosted reporter ion yield by up to 55%. Even so, unintended co-isolation of contaminating peaks in MS2 experiments distorts reporter ion intensities and can distort quantitative information. MS3 experiments address contamination by generating reporter ions via collisional activation (HCD) of one or more peptide product ions rather than the isolated peptide precursor ion. Because HCD performance is related to m/z, activation of multiple synchronously isolated product ions generates less than optimal reporter ion intensities. In this work, we show that using infrared multiphoton dissociation, which is not dependent on m/z, to generate reporter ions from 10 synchronously isolated peptide product ions results in a 2.4-fold increase in reporter ion intensities, significantly enhancing the sensitivity and dynamic range of quantitation via isobaric tagging.

Reactions of Arsenoplatin-1 with Protein Targets: A Combined Experimental and Theoretical Study.

Arsenoplatin-1 (AP-1) is a dual-action anticancer metallodrug with a promising pharmacological profile that features the simultaneous presence of a cisplatin-like center and an arsenite center. We investigated its interactions with proteins through a joint experimental and theoretical approach. The reactivity of AP-1 with a variety of proteins, including carbonic anhydrase (CA), superoxide dismutase (SOD), myoglobin (Mb), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and human serum albumin (HSA), was analyzed by means of electrospray ionization mass spectrometry (ESI MS) measurements. In accordance with previous observations, ESI MS experiments revealed that the obtained metallodrug–protein adducts originated from the binding of the [(AP-1)-Cl]+ fragment to accessible protein residues. Remarkably, in two cases, i.e., Mb and GAPDH, the formation of a bound metallic fragment that lacked the arsenic center was highlighted. The reactions of AP-1 with various nucleophiles side chains of neutral histidine, methionine, cysteine, and selenocysteine, in neutral form as well as cysteine and selenocysteine in anionic form, were subsequently analyzed through a computational approach. We found that the aquation of AP-1 is energetically disfavored, with a reaction free energy of +19.2 kcal/mol demonstrating that AP-1 presumably attacks its biological targets through the exchange of the chloride ligand. The theoretical analysis of thermodynamics and kinetics for the ligand-exchange processes of AP-1 with His, Met, Cys, Sec, Cys–, and Sec– side chain models unveils that only neutral histidine and deprotonated cysteine and selenocysteine are able to effectively replace the chloride ligand in AP-1.

Combining Isotopologue Workflows and Simultaneous Multidimensional Separations to Detect, Identify, and Validate Metabolites in Untargeted Analyses.

While the combination of liquid chromatography and tandem mass spectrometry (LC-MS/MS) is commonly used for feature annotation in untargeted omics experiments, ensuring these prioritized features originate from endogenous metabolism remains challenging. Isotopologue workflows, such as isotopic ratio outlier analysis (IROA), mass isotopomer ratio analysis of U-13C labeled extracts (MIRACLE), and credentialing incorporate isotopic labels directly into metabolic precursors, guaranteeing that all features of interest are unequivocal byproducts of cellular metabolism. Furthermore, comprehensive separation and annotation of small molecules continue to challenge the metabolomics field, particularly for isomeric systems. In this paper, we evaluate the analytical utility of incorporating ion mobility spectrometry (IMS) as an additional separation mechanism into standard LC-MS/MS isotopologue workflows. Since isotopically labeled molecules codrift in the IMS dimension with their 12C versions, LC-IMS-CID-MS provides four dimensions (LC, IMS, MS, and MS/MS) to directly investigate the metabolic activity of prioritized untargeted features. Here, we demonstrate this additional selectivity by showcasing how a preliminary data set of 30 endogeneous metabolites are putatively annotated from isotopically labeled Escherichia coli cultures when analyzed by LC-IMS-CID-MS. Metabolite annotations were based on several molecular descriptors, including accurate mass measurement, carbon number, annotated fragmentation spectra, and collision cross section (CCS), collectively illustrating the importance of incorporating IMS into isotopologue workflows. Overall, our results highlight the enhanced separation space and increased annotation confidence afforded by IMS for metabolic characterization and provide a unique perspective for future developments in isotopically labeled MS experiments.

Quantitative Mass Spectrometry Normalization in Urine Biomarker Analysis in Nephrotic Syndrome

Chronic kidney disease (CKD) affects 30 million adults, costs ∼$79 billion dollars (2016) in Medicare expenditures, and is the ninth leading cause of death in the USA. The disease is silent or undiagnosed in almost half of people with severely reduced kidney function. The urine provides an ideal biofluid that is accessible to high-sensitivity mass spectrometry-based proteomic interrogation and is an indicator of renal homeostasis. While the accurate and precise diagnosis and better disease management of CKD can be aided using urine biomarkers, their discovery in excessive protein or nephrotic urine samples can present challenges. In this work, we present a mass spectrometry-based method utilizing multiplex tandem mass tag (TMT) quantification and improved protein quantification using reporter ion normalization to urinary creatinine to analyze urinary proteins from patients with a form of nephrotic syndrome (focal segmental glomerulosclerosis [FSGS]). A comparative analysis was performed for urine from patients in remission (RM) versus active disease (DX) flare. Two-dimensional LC-MS/MS TMT quantitative analysis identified over 1,058 urine proteins and 580 proteins with 2 peptides or greater and quantifiable. Normalization of TMT abundance values to creatinine per ml of urine concentrated reduced variability in 2D-TMT-LC-MS/MS experiments. Univariate and multivariate analyses showed that 27 proteins were significantly increased in a proteinuric DX flare. Hierarchical heatmap clustering showed that SERPINA1 and ORM1 were increased >1.5-fold in active DX versus RM urine samples. ELISA validation of SERPINA1 and ORM1 abundance agreed with our quantitative TMT proteomics analysis. These findings provide support for the utility of this method for identification of novel diagnostic markers of CKD and identify SERPINA1 and ORM1 as promising candidate diagnostic markers for FSGS.

Cyclohumulanoid Sesquiterpenes Induced by the Noncompetitive Coculture of Phellinus orientoasiaticus and Xylodon flaviporus.

Microbial cocultivation has been applied as a strategy to induce the biosynthesis of specialized metabolites. However, most previous studies have focused on competitive interactions between test strains. During our LC-MS-based chemical screening of randomized cocultures of Basidiomycetous fungi, we discovered that the coculture of Phellinus orientoasiaticus (Hymenochaetaceae) and Xylodon flaviporus (Schizoporaceae) induces multiple metabolites, although they did not show any competitive morphology. Targeted isolation yielded three new sesquiterpenes (1-3) along with five known analogues (4-8). The structures of the isolates were determined by MS and NMR experiments as well as electronic circular dichroism analysis. LC-MS analysis suggested that cyclohumulanoids of illudane-, sterpurane-, and tremulane-type scaffolds (1-7) were produced by P. orientoasiaticus, whereas a drimane-type sesquiterpene (8) was produced by X. flaviporus. None of the isolates exhibited antifungal activity or cytotoxicity, and compounds 1-7 exhibited NO production of LPS-treated RAW276.4 cells in a range of 15.9% to 38.0% at 100 μM.

Seasonal variation of phenolic compounds in Zostera marina (Zosteraceae) from the Baltic Sea

Seasonal variations of phenolic compounds, in leaves of Zostera marina L. from the Baltic Sea near Kiel/Germany were investigated. Dominant compounds were mono- and disulfated flavonoids and phenylpropanoic acids, in particular luteolin 7,3ʹ-O-disulfate and diosmetin 7-O-sulfate as well as rosmarinic acid, a dimeric phenylpropanoid. All detected sulfated flavones showed similar seasonal trends: there were two significant concentration peaks in June and November. Moreover, two geographically distinct flavonoid chemotypes were identified based on their respective main flavonoid; one chemotype was characterized by the prevalence of luteolin 7,3ʹ-O-disulfate (German Baltic Sea), and the other by the prevalence of diosmetin 7-O-sulfate (Norwegian North Sea). Furthermore, an undescribed tetrameric phenylpropanoid, 7ʹʹ,8ʹʹ-didehydrosalvianolic acid B, was isolated and its structure was established by extensive NMR, MS, and CD experiments. This compound inhibited activity of Na+/K+-ATPase in the micro-molar range without any cytotoxic effects against human cancer and normal cells.

Quantitative analysis of polycyclic aromatic hydrocarbons using high-performance liquid chromatography-photodiode array-high-resolution mass spectrometric detection platform coupled to electrospray and atmospheric pressure photoionization sources.

Polycyclic aromatic hydrocarbons (PAHs) are common pollutants present in atmospheric aerosols and other environmental mixtures. They are of particular air quality and human health concerns as many of them are carcinogenic toxins. They also affect absorption of solar radiation by aerosols, therefore contributing to the radiative forcing of climate. For environmental chemistry studies, it is advantageous to quantify PAH components using the same analytical technics that are commonly applied to characterize a broad range of polar analytes present in the same environmental mixtures. Liquid chromatography coupled with photodiode array and high-resolution mass spectrometric detection (LC-PDA-HRMS) is a method of choice for comprehensive characterization of chemical composition and quantification of light absorption properties of individual organic compounds present in the environmental samples. However, quantification of non-polar PAHs by this method is poorly established because of their imperfect ionization in electrospray ionization (ESI) technique. This tutorial article provides a comprehensive evaluation of the quantitative analysis of 16 priority pollutant PAHs in a standard reference material using the LC-MS platform coupled with the ESI source. Results are further corroborated by the quantitation experiments using an atmospheric pressure photoionization (APPI) method, which is more sensitive for the PAH detection. The basic concepts and step-by-step practical guidance for the PAHs quantitative characterization are offered based on the systematic experiments, which include (1) Evaluation effects of different acidification levels by formic acid on the (+)ESI-MS detection of PAHs. (2) Comparison of detection limits in ESI+ versus APPI+ experiments. (3) Investigation of the PAH fragmentation patterns in MS2 experiments at different collision energies. (4) Calculation of wavelength dependent mass absorption coefficient (MACλ) of the standard mixture and its individual PAHs using LC-PDA data. (5) Assessment of the minimal injected mass required for accurate quantification of MACλ of the standard mixture and of a multi-component environmental sample.

Two new triterpenes isolated from Maytenus guangxiensis C. Y. Cheng et W. L. Sha and their antiproliferative activities

Two new triterpenes, 3β, 7β-dihydroxyolean-12-en-11-one (1) and 3β-O-acetyl-7β-hydroxyolean-12-en-11-one (2), along with four known triterpenes 3β-hydroxyolean-12-en-11-one (3), β-amyrin (4), lup-20(29)-ene-1β, 3β-diol (5) and 1β, 3β-dihydroxy-urs-9(11)-12-diene (6), were isolated from the stems and leaves of Maytenus guangxiensis C. Y. Cheng et W. L. Sha. Their structures were elucidated using 1D and 2D NMR spectroscopy as well as MS and IR experiments. Compounds (3-6) were isolated from M. guangxiensis for the first time. Compounds 1–6 were evaluated for their antiproliferative activities against Eca-109, PANC-1, EJ and HeLa cell lines. The results showed that compounds 1–6 displayed a certain degree of inhibitory effects against the proliferation of various human cancer cell lines.

Cucurbitane-type triterpenoids from the vines of Momordica charantia and their anti-inflammatory, cytotoxic, and antidiabetic activity

Phytochemical investigation of the ethanol extract from wild Momordica charantia vines has resulted in isolation of seven cucurbitane-type triterpenoids, including six undescribed compounds, kuguaovins H‒M, and the known compound, momordicoside K. The structures of the isolated compounds were elucidated on the basis of spectroscopic analyses, including 1D and 2D NMR, and MS experiments. The chemical structure of momordicoside K was determined for the first time by X-ray crystallographic analysis and its absolute configuration assigned. The cytotoxicity against four human tumor cell lines and anti-inflammatory activities on LPS-stimulated RAW264.7 macrophages were evaluated. Of the isolates, kaguaovin L exhibited potential cytotoxicity against MCF-7, HEp-2, Hep-G2, and WiDr cancer cell lines and showed moderate anti-NO production activity. In addition, kuguaovins H and J also showed the stimulatory effect of GLP-1 secretion on the murine intestinal secretin tumor cell line (STC-1).

Insight into the molecular basis of substrate recognition by the wall teichoic acid glycosyltransferase TagA

Wall teichoic acid (WTA) polymers are covalently affixed to the Gram-positive bacterial cell wall and have important functions in cell elongation, cell morphology, biofilm formation, and β-lactam antibiotic resistance. The first committed step in WTA biosynthesis is catalyzed by the TagA glycosyltransferase (also called TarA), a peripheral membrane protein that produces the conserved linkage unit, which joins WTA to the cell wall peptidoglycan. TagA contains a conserved GT26 core domain followed by a C-terminal polypeptide tail that is important for catalysis and membrane binding. Here, we report the crystal structure of the Thermoanaerobacter italicus TagA enzyme bound to UDP-N-acetyl-d-mannosamine, revealing the molecular basis of substrate binding. Native MS experiments support the model that only monomeric TagA is enzymatically active and that it is stabilized by membrane binding. Molecular dynamics simulations and enzyme activity measurements indicate that the C-terminal polypeptide tail facilitates catalysis by encapsulating the UDP-N-acetyl-d-mannosamine substrate, presenting three highly conserved arginine residues to the active site that are important for catalysis (R214, R221, and R224). From these data, we present a mechanistic model of catalysis that ascribes functions for these residues. This work could facilitate the development of new antimicrobial compounds that disrupt WTA biosynthesis in pathogenic bacteria.

UPLC-Q-TOF-MS/MS analysis of the guaiane sesquiterpenoids oxytropiols A-J and detection of undescribed analogues from the locoweed endophytic fungus Alternaria oxytropis (Pleosporaceae).

In addition to the mycotoxin swainsonine, the locoweed endophytic fungus Alternaria oxytropis (Pleosporaceae) also produces a series of rarely reported, highly oxygenated bicyclic guaiane sesquiterpenoids. Few investigations on the electrospray tandem mass fragmentation pattern of this sesquiterpenoid have been reported. We aimed to analyze and detect new guaiane sesquiterpenoid analogues from crude extracts of the locoweed endophytic fungus A. oxytropis by UPLC-Q-TOF-MS/MS experiments. Oxytropiols A-J (1-10) and the extract of the locoweed endophytic fungus A. oxytropis were analyzed by UPLC-Q-TOF-MS/MS in positive mode. Typical neutral losses, McLafferty rearrangement, 1,2-rearrangement, and 1,3-rearrangement were considered to be the main fragmentation patterns for the [M + H]+ /[M + Na]+ ions of 1-10 by UPLC-Q-TOF-MS/MS experiments, and possible fragmentation pathways of 1-10 were suggested. A unique and undescribed analogue named oxytropiol K (11) was found in the extract based on UPLC-Q-TOF-MS/MS analysis. Compound 11 was isolated and elucidated by NMR spectrometry, and its UPLC-Q-TOF-MS/MS analysis was consistent with the fragmentation pathways of 1-10. The results further support that UPLC-Q-TOF-MS/MS is a powerful and sensitive tool for the characterization of known compounds (dereplication) and the detection of new analogues from crude extracts and imply that the locoweed endophytic fungus A. oxytropis, with few chemical investigations, is an important resource for undescribed metabolites.

Lignans from the seeds of Herpetospermum pedunculosum and their farnesoid X receptor-activating effect

The seeds of Herpetospermum pedunculosum (Ser.) C.B. Clarke, a well-known Tibetan medicine in China, are rich in kinds of bioactive lignans. In this phytochemical investigation on H. pedunculosum, sixteen undescribed lignans, named as herpedulins A - P together with 24 known ones were isolated from the ethyl acetate extract of its seeds. Their structures including the absolute configurations were determined by HR MS, 1D and 2D NMR experiments, and comparison of their experimental ECD spectra with calculated ones or literature data. High content screening experiments revealed that 9 compounds could promote the expression of farnesoid X receptor in guggulsterone-induced human normal liver cells L02 cells significantly. Further molecular docking results demonstrated that herpedulin E, J and K exhibited best docking scores (9.70, 9.28 and 10.31, respectively). Hydrogen bonding and hydrophobic interactions might contribute to the main interaction of active compounds with FXR.

A new antimicrobial nor-friedelane-type triterpenoid and other constituents from Plectranthus glandulosus Hook. f. (Lamiaceae)

Chemical investigation of the ethanol extract from the whole plant of Plectranthus glandulosus led to the isolation of a new nor-triterpenoid (1) along with seventeen known compounds (2–18) including seven triterpenoids, nine flavonoids and one steroid. Their structures were established on the basis of 1D- and 2D-NMR, IR, and MS experiments, and by comparison of their spectroscopic data with those of similar compounds reported in the literature. The EtOH extract and some isolated triterpenoids (1–4 and 13) were subjected to in vitro antimicrobial assays against a panel of pathogenic microorganisms, including Gram-positive and Gram-negative bacteria, and fungi using broth microdilution method. The EtOH extract displayed moderate activity (MIC = 512 µg/mL) against Staphylococcus aureus MSSA1, Shigella flexneri SDINT and Cryptococcus neoformans H99. Compounds 1, 4 and 13 showed the most potent antimicrobial effect with MICs of 32–256 µg/mL.

The critical role of mobile phase pH in the performance of oligonucleotide ion-pair liquid chromatography-mass spectrometry methods.

The critical role of mobile phase pH in the performance of oligonucleotide ion-pair liquid chromatography-mass spectrometry methods.

Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity Quantification.

Enhanced in-source fragmentation/annotation (EISA) has recently been shown to produce fragment ions that match tandem mass spectrometry data across a wide range of small molecules. EISA has been developed to facilitate data-dependent acquisition (DDA), data-independent acquisiton (DIA), and multiple-reaction monitoring (MRM), enabling molecular identifications in untargeted metabolomics and targeted quantitative single-quadrupole MRM (Q-MRM) analyses. Here, EISA has been applied to peptide-based proteomic analysis using optimized in-source fragmentation to generate fragmentation patterns for a mixture of 38 peptides, which were comparable to the b- and y-type fragment ions typically observed in tandem MS experiments. The optimal in-source fragmentation conditions at which high-abundance peptide fragments and precursor ions coexist were compared with automated data-dependent acquisition (DDA) in the same quadrupole time-of-flight (QTOF-MS) mass spectrometer, generating a significantly higher fragment percentage of peptides from both singly and doubly charged b- and y-type fragment (b+, y+, b2+, and y2+) ions. Higher fragment percentages were also observed for these fragment ion series over linear ion trap instrumentation. An XCMS-EISA annotation/deconvolution program was developed, making use of the retention time and peak shape continuity between precursor fragment ions, to perform automated proteomic data analysis on the enhanced in-source fragments. Post-translational modification (PTM) characterization on peptides was demonstrated with EISA, producing fragment ions corresponding to a neutral loss of phosphoric acid with greater intensity than observed with DDA on a QTOF-MS. Moreover, Q-MRM demonstrated the ability to use EISA for peptide quantification. The availability of more sophisticated in-source fragmentation informatics, beyond XCMS-EISA, will further enable EISA for sensitive autonomous identification and Q-MRM quantitative analyses in proteomics.

Mass spectrometry analysis of saponins.

Saponins are amphiphilic molecules of pharmaceutical interest and most of their biological activities (i.e., cytotoxic, hemolytic, fungicide, etc.) are associated to their membranolytic properties. These molecules are secondary metabolites present in numerous plants and in some marine animals, such as sea cucumbers and starfishes. Structurally, all saponins correspond to the combination of a hydrophilic glycan, consisting of sugar chain(s), linked to a hydrophobic triterpenoidic or steroidic aglycone, named the sapogenin. Saponins present a high structural diversity and their structural characterization remains extremely challenging. Ideally, saponin structures are best established using nuclear magnetic resonance experiments conducted on isolated molecules. However, the extreme structural diversity of saponins makes them challenging from a structural analysis point of view since, most of the time, saponin extracts consist in a huge number of congeners presenting only subtle structural differences. In the present review, we wish to offer an overview of the literature related to the development of mass spectrometry for the study of saponins. This review will demonstrate that most of the past and current mass spectrometry methods, including electron, electrospray and matrix-assisted laser desorption/ionization ionizations, gas/liquid chromatography coupled to (tandem) mass spectrometry, collision-induced dissociation including MS3 experiments, multiple reaction monitoring based quantification, ion mobility experiments, and so forth, have been used for saponin investigations with great success on enriched extracts but also directly on tissues using imaging methods.

Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies.

Rhodesain is a major cysteine protease of Trypanosoma brucei rhodesiense, a pathogen causing Human African Trypanosomiasis, and a validated drug target. Recently, we reported the development of α-halovinylsulfones as a new class of covalent reversible cysteine protease inhibitors. Here, α-fluorovinylsulfones/-sulfonates were optimized for rhodesain based on molecular modeling approaches. 2d, the most potent and selective inhibitor in the series, shows a single-digit nanomolar affinity and high selectivity toward mammalian cathepsins B and L. Enzymatic dilution assays and MS experiments indicate that 2d is a slow-tight binder (Ki = 3 nM). Furthermore, the nonfluorinated 2d-(H) shows favorable metabolism and biodistribution by accumulation in mice brain tissue after intraperitoneal and oral administration. The highest antitrypanosomal activity was observed for inhibitors with an N-terminal 2,3-dihydrobenzo[b][1,4]dioxine group and a 4-Me-Phe residue in P2 (2e/4e) with nanomolar EC50 values (0.14/0.80 μM). The different mechanisms of reversible and irreversible inhibitors were explained using QM/MM calculations and MD simulations.