Xiaotao Duan

A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome.

For label-free expression profiling of tissue proteomes, efficient protein extraction, thorough and quantitative sample cleanup and digestion procedures, as well as sufficient and reproducible chromatographic separation, are highly desirable but remain challenging. However, optimal methodology has remained elusive, especially for proteomes that are rich in membrane proteins, such as the mitochondria. Here, we describe a straightforward and reproducible sample preparation procedure, coupled with a highly selective and sensitive nano-LC/Orbitrap analysis, which enables reliable and comprehensive expression profiling of tissue mitochondria. The mitochondrial proteome of swine heart was selected as a test system. Efficient protein extraction was accomplished using a strong buffer containing both ionic and nonionic detergents. Overnight precipitation was used for cleanup of the extract, and the sample was subjected to an optimized 2-step, on-pellet digestion approach. In the first step, the protein pellet was dissolved via a 4 h tryptic digestion under vigorous agitation, which nano-LC/LTQ/ETD showed to produce large and incompletely cleaved tryptic peptides. The mixture was then reduced, alkylated, and digested into its full complement of tryptic peptides with additional trypsin. This solvent precipitation/on-pellet digestion procedure achieved significantly higher and more reproducible peptide recovery of the mitochondrial preparation than observed using a prevalent alternative procedure for label-free expression profiling, SDS-PAGE/in-gel digestion (87% vs 54%). Furthermore, uneven peptide losses were lower than observed with SDS-PAGE/in-gel digestion. The resulting peptides were sufficiently resolved by a 5 h gradient using a nano-LC configuration that features a low-void-volume, high chromatographic reproducibility, and an LTQ/Orbitrap analyzer for protein identification and quantification. The developed method was employed for label-free comparison of the mitochondrial proteomes of myocardium from healthy animals versus those with hibernating myocardium. Each experimental group consisted of a relatively large number of animals (n = 10), and samples were analyzed in random order to minimize quantitative false-positives. With this approach, 904 proteins were identified and quantified with high confidence, and those mitochondrial proteins that were altered significantly between groups were compared with the results of a parallel 2D-DIGE analysis. The sample preparation and analytical strategy developed here represents an advancement that can be adapted to analyze other tissue proteomes.

Ultrasensitive Quantification of Serum Vitamin D Metabolites Using Selective Solid-Phase Extraction Coupled to Microflow Liquid Chromatography and Isotope-Dilution Mass Spectrometry

The capacity for quantification of active metabolites of vitamin D (VitD) is highly valuable to evaluate the risks and therapies for numerous diseases such as multiple sclerosis. However, the extremely low circulating levels and poor detectability of some dihydroxyl metabolites such as the 1alpha,25-dihydroxy-VitD(3) constitute a daunting challenge. Based on the combination of a selective solid-phase extraction (SPE) and a microflow liquid chromatography tandem mass spectrometry (microLC-MS/MS), we developed an ultrasensitive method for the robust, selective, and accurate quantification of four key VitD metabolites, including 25-hydroxy-VitD(2), 25-hydroxy-VitD(3), 24(R),25-dihydroxy-VitD(3), and 1alpha,25-dihydroxy-VitD(3), in serum samples. A one-step derivatization was employed to improve the ionization efficiency of the metabolites. The SPE procedure was optimized so that the analytes were selectively extracted from serum, while the sample matrix was substantially simplified. By eliminating majority of undesirable compounds from the matrix, the selective SPE enabled a high sample loading volume on the microLC column without causing overcapacity of the microLC column and thus helped to achieve ultralow detect limits in serum. An on-column sample focusing approach was employed to prevent band-broadening, and a sufficient microLC separation was achieved to eliminate endogenous interferences and to minimize ion suppression effect. Detect limits of the four metabolites ranged from 0.5-1 pg/mL, and the linearity was excellent for all compounds. The method showed high quantitative accuracy (error < 13.8%) and precision (CV < 14.1%). For 1alpha,25-dihydroxy-VitD(3), a lower limit of quantification (LLOQ) of 5 pg/mL was validated. This high level of sensitivity, for the first time, enabled the robust and consistent LC/MS/MS-based analysis of the four metabolites in a large-scale clinical investigation. Serum samples from 281 multiple sclerosis patients and 22 healthy subjects were analyzed, and it was discovered that the levels of both 24(R),25-dihydroxy-VitD(3) and 1alpha,25-dihydroxy-VitD(3) were significantly lower in patients than healthy subjects (P < 0.05). This novel observation may imply that the incidence of multiple sclerosis is inversely associated with the levels of the two metabolites. Moreover, the method was highly robust and reproducible as evaluated extensively in the clinical analysis; therefore, it could serve as a more selective and accurate alternative to immunoassay for large-scale clinical studies.

PHARMACOKINETICS AND METABOLISM OF THE FLAVONOID SCUTELLARIN IN HUMANS AFTER A SINGLE ORAL ADMINISTRATION

Scutellarin is widely used in treating various cardiovascular diseases. Few data are available regarding its metabolism and pharmacokinetics in humans. The objectives of this study were to develop methods to identify major metabolites of scutellarin in human urine and plasma and to determine simultaneously the parent drug and its major metabolites in human plasma for pharmacokinetic studies. Four metabolites were detected in urine samples by liquid chromatography coupled with electrospray multi-stage mass spectrometry (MS), but only one of them was found in plasma. Its structure was confirmed as scutellarein 6-O-β-d-glucuronide by MS, NMR, and UV absorbance spectra. The plasma concentrations of scutellarin and the major metabolite were simultaneously determined using liquid chromatography-tandem MS. After a single p.o. administration of 60 mg of scutellarin to 20 healthy subjects, the plasma concentrations of scutellarin were very low, and its plasma concentration-time curve was also anomalous. Plasma concentration of the major metabolite was comparatively high, and the peak plasma concentration was 87.0 ± 29.1 ng/ml. The Tmax was late (7.85 ± 1.62 h), and part of individual pharmacokinetic profiles showed double peaks, which indicated scutellarin could be absorbed into the intestine after hydrolysis to its aglycone by bacterial enzymes. This was followed by reconjugation in the intestinal cell and/or liver with glucuronic acid catalyzed by the phase II enzyme, which showed regioselectivity and species difference. The regioselectivity of glucuronoconjugation for scutellarin may be of importance for pharmacological activity. Plasma concentration of isoscutellarin can be used as a biomarker of scutellarin intake.

Vitamin D metabolites are associated with clinical and MRI outcomes in multiple sclerosis patients

Purpose The associations between vitamin D and MRI measures of brain tissue injury have not been previously investigated in multiple sclerosis (MS). This research evaluates the significance of vitamin D and its active metabolites in brain tissue injury and clinical disability in MS patients. Methods The study population consisted of 193 MS patients (152 women and 41 men; mean age 46.1 (SD 8.4) years; disease duration 13.8 (SD 8.4) years). Serum levels of 25-hydroxyvitamin D3 (25(OH)VD3), 25-hydroxyvitamin D2 (25(OH)VD2), 1α, 25-dihydroxyvitamin D3 (1, 25(OH)2VD3) and 24(R), 25-dihydroxyvitamin D3 (24, 25(OH)2VD3) were measured using a novel capillary liquid–chromatography–mass spectrometry method. Disability was assessed with the Expanded Disability Status Scale (EDSS) and the MS Severity Scale (MSSS). MRI measures included T2 lesion volume (LV), T1-LV and brain parenchymal fraction. The associations between deseasonalised levels of vitamin D metabolites and clinical and MRI measurements were assessed using regression analyses. Results Lower deseasonalised levels of total 25(OH)VD (p=0.029), 25(OH)VD3 (p=0.032) and 24, 25(OH)2VD3 (p=0.005) were associated with higher MSSS. Similarly, lower deseasonalised levels of 24, 25(OH)2VD3 (p=0.012) were associated with higher EDSS. Higher values of the 25(OH)VD3 to 24, 25(OH)2VD3 ratio were associated with higher MSSS (p=0.041) and lower brain parenchymal fraction (p=0.008). Conclusions Vitamin D metabolites have protective associations with disability and brain atrophy in MS. In particular, the results indicate strong associations for the 24, 25(OH)2VD3 metabolite, which has not been extensively investigated in MS patients.

Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and drbitrap mass spectrometry

Protein arginine (Arg) methylation serves an important functional role in eucaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron-transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679–695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z=2–4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns.

Environmental factors associated with disease progression after the first demyelinating event: results from the multi-center SET study.

Objectives To investigate the associations of environmental MS risk factors with clinical and MRI measures of progression in high-risk clinically isolated syndromes (CIS) after the first demyelinating event. Methods We analyzed 211 CIS patients (age: 28.9±7.8 years) enrolled in the SET study, a multi-center study of high-risk CIS patients. Pre-treatment samples were analyzed for IgG antibodies against cytomegalovirus (anti-CMV), Epstein Barr virus (EBV) early nuclear antigen-1 (EBNA-1), viral capsid antigen (VCA), early antigen-diffuse (EA-D), 25 hydroxy-vitamin D3 and cotinine levels and HLA DRB1*1501 status. The inclusion criteria required evaluation within 4 months of the initial demyelinating event, 2 or more brain MRI lesions and the presence of two or more oligoclonal bands in cerebrospinal fluid. All patients were treated with interferon-beta. Clinical and MRI assessments were obtained at baseline, 6, 12, and 24 months. Results The time to first relapse decreased and the number of relapses increased with anti-CMV IgG positivity. Smoking was associated with increased number and volume of contrast-enhancing lesions (CEL) during the 2-year period. The cumulative number of CEL and T2 lesions during the 2-year period was greater for individuals in the highest quartile of anti-EBV VCA IgG antibodies. The percent loss of brain volume was increased for those in the highest quartile of with anti-EBV VCA IgG antibodies. Conclusions Relapses in CIS patients were associated with CMV positivity whereas anti-EBV VCA positivity was associated with progression on MRI measures, including accumulation of CEL and T2 lesions and development of brain atrophy.

A Rapid, Reproducible, On-the-Fly Orthogonal Array Optimization Method for Targeted Protein Quantification by LC/MS and Its Application for Accurate and Sensitive Quantification of Carbonyl Reductases in Human Liver

Liquid chromatography (LC)/mass spectrometry (MS) in selected-reactions-monitoring (SRM) mode provides a powerful tool for targeted protein quantification. However, efficient, high-throughput strategies for proper selection of signature peptides (SP) for protein quantification and accurate optimization of their SRM conditions remain elusive. Here we describe an on-the-fly, orthogonal array optimization (OAO) approach that enables rapid, comprehensive, and reproducible SRM optimization of a large number of candidate peptides in a single nanoflow-LC/MS run. With the optimized conditions, many peptide candidates can be evaluated in biological matrixes for selection of the final SP. The OAO strategy employs a systematic experimental design that strategically varies product ions, declustering energy, and collision energy in a cycle of 25 consecutive SRM trials, which accurately reveals the effects of these factors on the signal-to-noise ratio of a candidate peptide and optimizes each. As proof of concept, we developed a highly sensitive, accurate, and reproducible method for the quantification of carbonyl reductases CBR1 and CBR3 in human liver. Candidate peptides were identified by nano-LC/LTQ/Orbitrap, filtered using a stringent set of criteria, and subjected to OAO. After evaluating both sensitivity and stability of the candidates, two SP were selected for quantification of each protein. As a result of the accurate OAO of assay conditions, sensitivities of 80 and 110 amol were achieved for CBR1 and CBR3, respectively. The method was validated and used to quantify the CBRs in 33 human liver samples. The mean level of CBR1 was 93.4 +/- 49.7 (range: 26.2-241) ppm of total protein, and of CBR3 was 7.69 +/- 4.38 (range: 1.26-17.9) ppm. Key observations of this study: (i) evaluation of peptide stability in the target matrix is essential for final selection of the SP; (ii) utilization of two unique SP contributes to high reliability of target protein quantification; (iii) it is beneficial to construct calibration curves using standard proteins of verified concentrations to avoid severe biases that may result if synthesized peptides alone are used. Overall, the OAO method is versatile and adaptable to high-throughput quantification of validated biomarkers identified by proteomic discovery experiments.

Nano-scale Liquid Chromatography/Mass Spectrometry and On-the-fly Orthogonal Array Optimization for Quantification of Therapeutic Monoclonal Antibodies and the Application in Preclinical Analysis

Therapeutic monoclonal antibodies (mAbs) constitute a group of highly effective agents for treating various refractory diseases. Nonetheless it is challenging to achieve selective and accurate quantification of mAb in pharmaceutical matrices, which is required by PK studies. Liquid chromatography/mass spectrometry under selected reaction monitoring mode (LC/SRM-MS) is emerging as an attractive alternative to immunoassays because of the high specificity and multiplexing capacity it provides, but may fall short in terms of sensitivity, reliability and quantitative accuracy. Moreover, the strategy for optimization of the MS conditions for many candidates of signature peptides (SP) and the selection of the optimal SP for quantification remains elusive. In this study, we employed a suite of technical advances to overcome these difficulties, which include: (i) a nano-LC/SRM-MS approach to achieve high analytical sensitivity, (ii) a high-resolution nano-LC/LTQ/Orbitrap for confident identification of candidate peptides, (iii) an on-the-fly orthogonal array optimization (OAO) method for the high-throughput, accurate and reproducible optimization for numerous candidate peptides in a single LC/MS run without using synthesized peptides, (iv) a comprehensive evaluation of stability of candidates in matrix using the optimized SRM parameters, (v) the use of two unique SP for quantification of one mAb to gauge possible degradation/modification in biological system and thus enhancing data reliability (e.g. rejection of data if the deviation between the two SP is greater than 25%) and (vi) the utilization of purified target protein as the calibrator to eliminate the risk of severe negative biases that could occur when a synthesized peptide is used as calibrator. To show a proof of concept, this strategy is applied in the quantification of cT84.66, a chimeric, anti-CEA antibody, in preclinical mouse models. A low detection limit of the mAb down to 3.2 ng/mL was achieved, which is substantially more sensitive than established immunoassay methods for anti-CEA antibodies. The quantitative method showed good linearity (within the range of 12.9 ng/mL to 32.3 μg/mL in plasma), accuracy and precision. Additionally, the ultra-low sample consumption (2 μL plasma per preparation) permits the acquisition of an entire set of time course data from the same mouse, which represents a prominent advantage for PK study using small-animal models. The developed method enabled an accurate PK investigation of cT84.66 in mice following intravenous and subcutaneous administrations at relatively low doses over an extended period of time. The strategy employed in this study can be easily adapted to the sensitive and accurate analysis of other mAb and therapeutic proteins.

Highly multiplexed and reproducible ion-current-based strategy for large-scale quantitative proteomics and the application to protein expression dynamics induced by methylprednisolone in 60 rats.

A proteome-level time-series study of drug effects (i.e., pharmacodynamics) is critical for understanding mechanisms of action and systems pharmacology, but is challenging, because of the requirement of a proteomics method for reliable quantification of many biological samples. Here, we describe a highly reproducible strategy, enabling a global, large-scale investigation of the expression dynamics of corticosteroid-regulated proteins in livers from adrenalectomized rats over 11 time points after drug dosing (0.5–66 h, N = 5/point). The analytical advances include (i) exhaustive tissue extraction with a Polytron/sonication procedure in a detergent cocktail buffer, and a cleanup/digestion procedure providing very consistent protein yields (relative standard deviation (RSD%) of 2.7%–6.4%) and peptide recoveries (4.1–9.0%) across the 60 animals; (ii) an ultrahigh-pressure nano-LC setup with substantially improved temperature stabilization, pump-noise suppression, and programmed interface cleaning, enabling excellent reproducibility for continuous analyses of numerous samples; (iii) separation on a 100-cm-long column (2-μm particles) with high reproducibility for days to enable both in-depth profiling and accurate peptide ion-current match; and (iv) well-controlled ion-current-based quantification. To obtain high-quality quantitative data necessary to describe the 11 time-points protein expression temporal profiles, strict criteria were used to define “quantifiable proteins”. A total of 323 drug-responsive proteins were revealed with confidence, and the time profiles of these proteins provided new insights into the diverse temporal changes of biological cascades associated with hepatic metabolism, response to hormone stimuli, gluconeogenesis, inflammatory responses, and protein translation processes. Most profile changes persisted well after the drug was eliminated. The developed strategy can also be broadly applied in preclinical and clinical research, where the analysis of numerous biological replicates is crucial.

Effects of Calibration Approaches on the Accuracy for LC–MS Targeted Quantification of Therapeutic Protein

LC–MS provides a promising alternative to ligand-binding assays for quantification of therapeutic proteins and biomarkers. As LC–MS methodology is based on the analysis of proteolytic peptides, calibration approaches utilizing various calibrators and internal standards (I.S.) have been developed. A comprehensive assessment of the accuracy and reliability of these approaches is essential but has yet been reported. Here we performed a well-controlled and systematic comparative study using quantification of monoclonal-antibody in plasma as the model system. Method development utilized a high-throughput orthogonal-array-optimization, and two sensitive and stable signature-peptides (SP) from different domains were selected based on extensive evaluations in plasma matrix. With the purities of all protein/peptide standards corrected by quantitative amino acid analysis (AAA), five calibration approaches using stable-isotope-labeled (SIL) I.S. were thoroughly compared, including those at peptide, extended-peptide, and protein levels and two “hybrid” approaches (i.e., protein calibrator with SIL-peptide or SIL-extended-peptide I.S.). These approaches were further evaluated in parallel for a 15 time point, preclinical pharmacokinetic study. All methods showed good precision (CV% < 20%). When examined with protein-spiked plasma QC, peptide-level calibration exhibited severe negative biases (−23 to −62%), highly discordant results between the two SP (deviations of 38–56%), and misleading pharmacokinetics assessments. Extended-peptide calibration showed significant improvements but still with unacceptable accuracy. Conversely, protein-level and the two hybrid calibrations achieved good quantitative accuracy (error < 10%), concordant results by two SP (deviations < 15%), and correct pharmacokinetic parameters. Hybrid approaches were found to provide a cost-effective means for accurate quantification without the costly SIL-protein. Other key findings include (i) using two SP provides a versatile gauge for method reliability; (ii) evaluation of peptide stability in the matrix before SP selection is critical; and (iii) using AAA to verify purities of protein/peptide calibrators ensures accurate quantitation. These results address fundamental calibration issues that have not been adequately investigated in published studies and will provide valuable guidelines for the “fit for purpose” development of accurate LC–MS assays for therapeutic proteins and biomarkers in biological matrices.