Recent advances in top-down proteome sample processing ahead of MS analysis.

Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.

Enantioselective degradation of hexaconazole in rat hepatic microsomes in vitro.

Hexaconazole [(RS)-2-(2,4-dichlorophenyl)-1-(1H-1,2,4-triazol-1-yl) hexan-2-ol] is a potent triazole fungicide and consists of a pair of enantiomers. Enantioselective degradation of hexaconazole was investigated in rat hepatic microsomes in vitro. Concentrations of (-)- and (+)-hexaconazole and enantiomer fraction were determined by high performance liquid chromatography with a cellulose-tris-(3,5-dimethylphenylcarbamate)-based chiral stationary phase. The t(1/2) of (-)-hexaconazole and (+)-hexaconazole were 23.70 and 13.95 min for rac- hexaconazole and 44.18 and 23.54 for enantiomers examined separately. Furthermore, hexaconazole is configurationally stable in rat hepatic microsomes, demonstrating no chiral inversion from the (-)-hexaconazole to (+)-hexaconazole or vice versa. Intrinsic metabolic clearance of (+)-hexaconazole is 1.12 times than that of (-)-hexaconazole. Interaction study revealed that there was competitive inhibition between (-)-hexaconazole and (+)-hexaconazole. In addition, there was a significant difference between the inhibitory concentration (IC(50)) of (-)- to (+)-hexaconazole and (+)- to (-)-hexaconazole [IC(50)(-)/(+)/IC(50)(+)/(-) = 1.88]. These results may have potential implications for better environmental and ecological risk assessment for hexaconazole.

Stereoselective degradation of metalaxyl and its enantiomers in rat and rabbit hepatic microsomes in vitro.

The stereoselective degradations of racemate metalaxyl (rac-MX) and its single enantiomers in rat and rabbit hepatic microsomes were assayed by a chiral high-performance liquid chromatography method. The t(1/2) of (+)-S-MX in rat liver microsomes was between 7-8 min tested by rac-MX and the individual (+)-S-enantiomer, respectively, and that for (-)-R-MX was 15-16 min. In contrast, t(1/2) in rabbit liver microsomes was much longer and showed great difference when using racemate and single enantiomer, which was similar to the results of in vivo study. The enantioselectivity in rat hepatic microsomes was more evident and the degradations of MX enantiomers in rat and rabbit hepatic microsomes were Nicotinamide adenine dinucleotide phosphate-dependent. Michaelis constant (K(m)) and intrinsic metabolic clearance (CL(int)) of (+)-S-MX were larger than that of (-)-R-MX and there was no chiral inversion from (+)-S-MX to (-)-R-MX or vice versa in both rat and rabbit hepatic microsomes.

Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry.

While multiple advances in mass spectrometry (MS) instruments have improved qualitative and quantitative proteome analysis, more reliable front-end approaches to isolate, enrich, and process proteins ahead of MS are critical for successful proteome characterization. Low, inconsistent protein recovery and residual impurities such as surfactants are detrimental to MS analysis. Protein precipitation is often considered unreliable, time-consuming, and technically challenging to perform compared to other sample preparation strategies. These concerns are overcome by employing optimal protein precipitation protocols. For acetone precipitation, the combination of specific salts, temperature control, solvent composition, and precipitation time is critical, while the efficiency of chloroform/methanol/water precipitation depends on proper pipetting and vial manipulation. Alternatively, these precipitation protocols are streamlined and semi-automated within a disposable spin cartridge. The expected outcomes of solvent-based protein precipitation in the conventional format and using a disposable, two-stage filtration and extraction cartridge are illustrated in this work. This includes the detailed characterization of proteomic mixtures by bottom-up LC-MS/MS analysis. The superior performance of SDS-based workflows is also demonstrated relative to non-contaminated protein.

Stereoselective metabolism of benalaxyl in liver microsomes from rat and rabbit.

Benalaxyl (BX), methyl-N-phenylacetyl-N-2,6-xylyl alaninate, is a potent acylanilide fungicide and consist of a pair of enantiomers. The stereoselective metabolism of BX was investigated in rat and rabbit microsomes in vitro. The degradation kinetics and the enantiomer fraction (EF) were determined using normal high-performance liquid chromatography with diode array detection and a cellulose-tris-(3,5-dimethylphenylcarbamate)-based chiral stationary phase (CDMPC-CSP). The t(1/2) of (-)-R-BX and (+)-S-BX in rat liver microsomes were 22.35 and 10.66 min of rac-BX and 5.42 and 4.03 of BX enantiomers. However, the t(1/2) of (-)-R-BX and (+)-S-BX in rabbit liver microsomes were 11.75 and 15.26 min of rac-BX and 5.66 and 9.63 of BX enantiomers. The consequence was consistent with the stereoselective toxicokinetics of BX in vitro. There was no chiral inversion from the (-)-R-BX to (+)-S-BX or inversion from (+)-S-BX to (-)-R-BX in both rabbit and rat microsomes. These results suggested metabolism of BX enantiomers was stereoselective in rat and rabbit liver microsomes.

Stereoselective pharmacokinetics of diniconazole enantiomers in rabbits.

Diniconazole [(E)-(RS)-1-(2,4,-dichlorophenyl)-4,4-dimethyl-2-(1H-1,2,4-triazole-1-yl)pent-1-en-3-ol)] is a potent triazole fungicide. The enantioselective pharmacokinetics of diniconazole enantiomers in rabbits was studied via intravenous (i.v.) injection. The pharmacokinetics and the enantiomer fraction (EF) were determined using normal high-performance liquid chromatography with diode array detection and a cellulose-tris-(3,5-dimethylphenylcarbamate)-based chiral stationary phase (CDMPC-CSP). The time-concentration curves in plasma were fitted by a two-compartment open mode. The results showed that the concentration of S-diniconazole in plasma decreased faster than that of R-diniconazole, and EFs increased with time after administration of racemic diniconazole (rac-diniconazole). The R-/S-enantiomer ratio of the area under the time-plasma concentration curve (AUC(0-infinity)) after administration was 1.52. The total plasma clearance value of S-enantiomer was 1.57-fold higher than that of the R-diniconazole. These results indicate substantial stereoselectivity in the kinetics of diniconazole enantiomers in rabbit.

Enantioselective behavior of malathion enantiomers in toxicity to beneficial organisms and their dissipation in vegetables and crops.

The dissipation behavior of the two enantiomers of malathion was elucidated in five plant species using enantioselective high performance liquid chromatography (HPLC), and the acute toxicity of the individual enantiomers toward earthworms and honeybees was studied. The calculated LC(50) values of the R-, S- and rac-malathion to earthworms were 0.3869, 25.17, and 19.19 µg/cm(2), respectively, while the calculated LC(50) values of R-, S- and rac-malathion to bees were 2.15, 36.67, and 7.11 µg/mL, respectively. This indicated that the R-enantiomer was more toxic than S-enantiomer. The results of the degradation of racemate in Chinese cabbage and rape showed that the inactive S-(-)-enantiomer degraded faster than the active R-(+)-enantiomer. Inversely, we found a preferential degradation of the R-(+)-enantiomer in sugar beet. However, the degradation of malathion in paddy rice and wheat were nonenantioselectivity. In all plants, malathion was degraded to levels <10% after 5 days, and the calculated t(½) values of the enantiomers ranged from 0.83 to 1.43 days in these five plants. In conclusion, our findings of enantioselectivity in the environmental fate and acute toxicity of the malathion enantiomers may have implications for better environmental and ecological risk assessment for chiral pesticides in general.

Influence of soil properties on the enantioselective dissipation of the herbicide lactofen in soils.

A scheme was developed to elucidate the dissipation behaviors of the two enantiomers of the herbicide lactofen in soils using a normal-phase high-performance liquid chromatograph (HPLC) with UV detector and a column with a cellulose-tri-(3,5-dimethylphenylcarbamate)-based chiral stationary phase (CDMPC-CSP). Eight soils with a wide range of soil properties were studied. Racemic and the enantiopure (S)-(+)- and (R)-(-)-lactofen were incubated under aerobic and anaerobic conditions. The data from sterilized controls indicated that the dissipation of lactofen was biological. The dissipation was shown to be enantioselective with (S)-(+)-enantiomer being degraded faster than the (R)-(-)-enantiomer, resulting in residues enriched with (R)-(-)-lactofen when the racemic compound was incubated. Lactofen was configurationally stable in soil, showing no interconversion of (S)-(+)- to (R)-(-)- enantiomer and vice versa. Significant correlations of the enantioselectivity, expressed as ES = (k((S)) - k((R)))/(k((S)) + k((R))) of lactofen with soil pH were observed under aerobic and anaerobic conditions. In addition, we found that the enantioselectivity correlated with the soil texture rather than the organic carbon.

Stereoselective degradation kinetics of tebuconazole in rabbits.

Tebuconazole[(RS)-1-p-chlorophenyl-4,4-dimethyl-3-(1H-1,2,4-triazol-1-ylmethyl)pentan-3-ol] is a potent triazole fungicide and consists of a pair of enantiomers. The enantioselective degradation kinetics of tebuconazole was investigated in rabbits by intravenous (iv) injection. The concentrations of (-)-(R)-tebuconazole and (+)-(S)-tebuconazole in plasma and tissues were determined by HPLC with a cellulose tris(3,5-dimethylphenylcarbamate)-based chiral stationary phase. Enantioselective analysis methods for this fungicide in plasma and tissues were developed and validated. Good linearities were obtained over the concentration range of 0.25-25 mg/l for both enantiomers. The degradation followed pseudo-first-order kinetics and the degradation of the (+)-(S)-tebuconazole was much faster than that of the (-)-(R)-tebuconazole in plasma after administration of racemic tebuconazole. This study also indicated that environmental assessment of enantiomeric degradation may be needed to fully evaluate risks of tebuconazole use.

Stereoselective toxicokinetics and tissue distribution of ethofumesate in rabbits.

The stereoselective toxicokinetics of ethofumesate enantiomers following a single intravenous (i.v.) administration at doses of 30 mg/kg were investigated in rabbits. Plasma concentrations of (+)- and (-)-ethofumesate were analyzed by a validated chiral HPLC method that involved extraction of plasma with organic solvent followed by separation on a cellulose-Tris-(3,5-dimethylphenylcarbamate)-based chiral column and quantification by UV absorbance at 230 nm. Plasma concentration-time curves after i.v. administration were best described by an open two-compartment model. The concentration of the (-)-enantiomer decreased more rapidly than that of the (+)-enantiomer. Significant differences in toxicokinetic parameters between the two enantiomers indicated that stereoselective behavior occurred with the (-)-enantiomer being preferentially metabolized and eliminated.