Neuropeptidomics: Comparison of parallel reaction monitoring and data‐independent acquisition for the analysis of neuropeptides using high‐resolution mass spectrometry

Targeted peptide quantitation by mass spectrometry is a rapidly emerging field. Traditionally it relied on the development and validation of multiple reaction monitoring assays that could comply with a high level of sensitivity, specificity, accuracy and reproducibility in complex biological samples. However, with the introduction of high‐resolution mass spectrometers, other acquisition modes could provide more comprehensive datasets for identification and quantification but also for in‐depth data mining. The objective of this study was to evaluate two analytical approaches, parallel‐reaction monitoring (PRM) and data‐independent analysis (DIA) using a hybrid Quadrupole–Orbitrap mass spectrometer for the quantification of neuropeptides in animal spinal cord tissues. Mouse spinal cord tissues were harvested, homogenized and neuropeptides extracted using a C₁₈ solid‐phase extraction protocol. Chromatography was achieved using a Thermo Biobasic C₈ 100 × 1 mm (5 μm) column. The initial mobile phase conditions consisted of acetonitrile and water (both containing 0.1% of formic acid) at a ratio of 5:95. An 11 min linear gradient was applied up to a ratio of 50:50 and maintained for 3 min. The flow rate was fixed at 75 μL/min and 2 μL of sample was injected. Mass spectrometry analyses were performed using a Thermo Q Exactive Plus MS using PRM and DIA approaches. Quantitative data using an isotopic dilution and a label‐free strategy were obtained for both methods and statistically compared. Using both approaches, we were able to clearly detect endogenous neuropeptides. However, with DIA, mass spectra alone could not distinguish Leu‐Enk and Met‐Enk. We used a Bland–Altman plot (Difference plot) to analyze the agreement between both approaches and no systematic bias was observed. Further statistical analyses, including variance analysis, showed more variability in DIA compared with PRM mode. Further analyses were performed using a label‐free approach and confirmed an increase of the variance using a DIA approach.     

Stable isotope dilution assay for the accurate determination of tricaine in fish samples by HPLC–MS–MS

Tricaine methanesulfonate is one of most commonly used anesthetics in fish during blood sampling, artificial propagation and long‐distance transportation. In this study, an accurate method for the quantitative determination of tricaine in fish samples by a stable isotope dilution assay coupled with high‐performance liquid chromatography–triple quadrupole mass spectrometry was developed. Tricaine‐D₅ was synthesized and used as an isotopically labeled internal standard for the determination of tricaine. The analytical performance of the method was validated for tricaine determination in marine fish and freshwater fish. The determination of tricaine was linear in the range of 2.0–200.0 μg L^?1. The limit of detection and limit of quantitation for fish muscle tissues were 1.0 and 4.0 μg kg^?1, respectively. Good recoveries were obtained in the range of 92.08–97.50%. The inter‐ and intra‐assay relative standard deviations (RSD values) were investigated, and the values were 0.39–3.01 and 0.85–2.77%, respectively. The values of CCα and CCβ were 10.21–10.43 and 10.42–10.87 μg kg^?1, respectively. The clearance of MS‐222 from grass carp was further studied using our method. The results demonstrate that MS‐222 could be well absorbed and rapidly eliminated after bath administration.     

MeCAT peptide labeling for the absolute quantification of proteins by 2D‐LC‐ICP‐MS

Metal‐Coded Affinity Tags (MeCAT) reagents were devised for the absolute quantification of labeled proteins and peptides using inductively coupled plasma mass spectrometry (ICP‐MS). After the recent publication of quantification approaches for digested proteins, this work presents a multidimensional strategy for the application of MeCAT to samples which require higher chromatographic resolution. Two‐dimensional separations based on strong cation exchange (SCX) and reversed‐phase (RP) chromatography, were used for the quantification of lysozyme, bovine serum albumin and transferrin after tryptic digestion. The elution protocols were optimized to improve the resolution of the MeCAT‐labeled peptides which led to faster elutions in SCX and longer retention times in RP compared with unlabeled peptides. The optimized method provided enough resolution for the samples analyzed. Peptides losses during the whole procedure were studied. Although recoveries of greater than 90% were found in the RP dimension, important global losses in the two‐dimensional offline approach forced us to use specific internal standards, in this case MeCAT‐labeled standard peptides. External calibration and label‐specific isotope dilution analysis (IDA) were tested and compared as possible quantification techniques. While both techniques showed accurate and precise determinations, the label‐specific IDA technique resulted in more straightforward measurements and more affordable external calibrations. Finally, simultaneous quantification of three different samples labeled with different lanthanides was successfully performed demonstrating the potential of MeCAT combined with ICP‐MS for multiplexing. Electrospray ionization mass spectrometry techniques provided the structural information needed for the identification of the labeled species. Copyright © 2012 John Wiley & Sons, Ltd.     

HPLC-CHIP coupled to a triple quadrupole mass spectrometer for carbonic anhydrase II quantification in human serum

A method for carbonic anhydrase II (CA II) absolute quantification in human serum is presented. This method is based on high-performance liquid chromatography (HPLC)-Chip microfluidic device incorporating a nanoelectrospray source interfaced to a triple quadrupole mass spectrometer. The fraction containing CA II was isolated by preparative reversed-phase HPLC, and peptides obtained from the tryptic digest of the protein mixture were separated by the HPLC-Chip system. The multiple-reaction monitoring acquisition mode of a selected suitable CA II peptide and peptide internal standard allowed the selective and sensitive determination of a CA II. Absolute recovery of the method was 52 ± 12%, while analytical recovery was 81 ± 10%. For the eight samples analyzed, the matrix effect was found to be only −14 ± 6%. A comparison among three regression lines type which were obtained by external calibration, matrix-matched calibration, and standard addition method, respectively, demonstrated that the first one is adequate in obtaining good accuracy and precision. Method quantification limit for CA II in serum was estimated to be 2 fmol/mL. CA II mean concentration in sera from eight healthy subjects was found to be 56 pmol/mL (relative standard deviation 24%).     

Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications

In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)‐based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS‐based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow‐up. Copyright © 2016 John Wiley & Sons, Ltd.     

Joint MS‐based platforms for comprehensive comparison of rat plasma and serum metabolic profiling

Metabolomics is a rapidly growing field in the comprehensive understanding of cellular and organism‐specific responses associated with perturbations induced by medicines, chemicals and environment. Blood matrices are frequently used in clinical and biological studies. In this study, we compared metabolic profiling between rat plasma and serum using complementary platforms of gas chromatography–mass spectrometry (GC‐MS) and liquid chromatography–quadruple time‐of‐flight–mass spectrometry (LC‐QTOF‐MS). The sample types that were tested included plasma prepared with K₂EDTA and serum collected using venous blood collection protocols. The results of peak area variation for each detected metabolite/feature in the quality control samples showed a good reproducibility in LC‐QTOF‐MS and better reproducibility in GC‐MS. In GC‐MS analysis: (a) 25.8% of the defined metabolites differed serum from plasma profiling (t‐test, p < 0.05); and (b) serum possessed higher sensitivity than plasma for its generally higher peak intensity in the metabolic profiling. In LC‐QTOF‐MS analysis, 13 (in positive ion mode) and seven (in negative ion mode) important metabolites were identified as mainly contributing to the separation between serum and plasma. Copyright © 2014 John Wiley & Sons, Ltd.     

Discovery of false identification using similarity difference in GC–MS‐based metabolomics

Compound identification is a critical process in metabolomics. The widely used approach for compound identification in gas chromatography–mass spectrometry‐based metabolomics is spectrum matching, in which the mass spectral similarity between an experimental mass spectrum and each mass spectrum in a reference library is calculated. While various similarity measures have been developed to improve the overall accuracy of compound identification, little attention has been paid to reducing the false discovery rate. We, therefore, develop an approach for controlling the false identification rate using the distribution of the difference between the first and second highest spectral similarity scores. We further propose a model‐based approach to achieving a desired true positive rate. The developed method is applied to the National Institute of Standards and Technology mass spectral library, and its performance is compared with that of the conventional approach that uses only the maximum spectral similarity score. The results show that the developed method achieves a significantly higher F1 score and positive predictive value than did the conventional approach. Copyright © 2014 John Wiley & Sons, Ltd.     

Static SIMS–VAMAS interlaboratory study for intensity repeatability,mass scale accuracy and relative quantification

An interlaboratory study involving 19 time‐of‐flight static secondary ion mass spectrometer (TOF‐SSIMS) instruments from 12 countries has been conducted. Analysts were supplied, by the National Physical Laboratory, with a protocol for analysis together with three reference materials: poly(tetrafluoroethylene), a thin layer of polycarbonate on a silicon wafer and a patterned sample with different amounts of Irganox 1010 in each of four quadrants on a silicon wafer. The objectives of the study are (i) to determine the repeatability and constancy of the relative intensity scale achievable using the draft ISO standard (DIS 23830), (ii) to evaluate the effectiveness of mass scale calibration and optimisation procedure and (iii) to evaluate the current capability of relative quantification using SSIMS. The results of this study show that the constancy of the relative intensity scale has an approximate scatter standard deviation of only 5%. This is excellent and demonstrates that SSIMS measurements are significantly more stable than often thought by analysts. The draft ISO standard (DIS) CD 13084 for calibration of the mass scale in TOF‐SIMS was evaluated and found to be consistent with our previous study. Four laboratories optimised the instrument mass calibration accuracy using this procedure leading to improvements in mass scale calibration by factors of 1.8, 2.2, 2.3 and 8.6. Using a novel patterned Irganox sample it is shown that the precision of relative quantification may be as good as a standard deviation of only 5% for 16 instruments—this is a remarkable result. Further work is required to develop more robust reference materials. © Crown copyright 2010. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.     

MSn,LC‐MS‐TOF and LC‐PDA studies for identification of new degradation impurities of bupropion

Three new degradation impurities of bupropion were characterized through high performance liquid chromatography coupled to photodiode array detection and to time‐of‐flight mass spectrometry. Bupropion was subjected to the ICH prescribed stress conditions. It degraded to seven impurities (I–VII) in alkaline hydrolytic conditions which were optimally resolved on an XTerra C₁₈ column (250 × 4.6 mm, 5 µm) with a ternary mobile phase comprising ammonium formate (20 mm , pH 4.0), methanol and acetonitrile (75:10:15, v/v). The degradation impurities (III–V and VII) were characterized on the basis of mass fragmentation pattern of drug, accurate mass spectral and photodiode array data of the drug and degradation impurities. Compound V was found to be a known degradation impurity [1‐hydroxy‐1‐(3‐chlorophenyl)propan‐2‐one], whereas III, IV and VII were characterized as 2‐hydroxy‐2‐(3′‐chlorophenyl)‐3,5,5‐trimethylmorpholine, (2,4,4‐trimethyl‐1,3‐oxazolidin‐2‐yl)(3‐chlorophenyl)‐methanone and 2‐(3′‐chlorophenyl)‐3,5,5‐trimethylmorphol‐2‐ene, respectively. Compound III was a known metabolite of the drug. This additional information on the degradation impurities can help in the development of a new stability‐indicating assay method to monitor the stability of the drug product during its shelf‐life as well as in development of a drug product with increased shelf‐life. Copyright © 2013 John Wiley & Sons, Ltd.     

Critical evaluation of screening techniques for emerging environmental contaminants based on accurate mass measurements with time‐of‐flight mass spectrometry

Emerging contaminants from wastewater effluent samples were analysed, using posttarget and nontarget analysis techniques. The samples were analysed with an ultra performance liquid chromatograph‐time‐of‐flight mass spectrometer (UPLC‐TOF‐MS), and the resulting data were processed with commercial deconvolution software. The method works well for posttarget analysis with prior information about the retention times of the compounds of interest. With positive polarity, 63 of 66 compounds and with negative polarity, 18 of 20 compounds were correctly identified in a spiked sample, while two compounds of a total of 88 fell out of the mass range. Furthermore, a four‐stage process for identification was developed for the posttarget analysis lacking the retention time data. In the process, the number of candidate compounds was reduced by using the accurate mass of selected compounds in two steps (stages 1 and 2), structure–property relationships (stage 3) and isotope patterns of the analytes (stage 4). The process developed was validated by analysing wastewater samples spiked with 88 compounds. This procedure can be used to gain a preliminary indication of the presence of certain analytes in the samples. Nontarget analysis was tested by applying a theoretical mass spectra library for a wastewater sample spiked with six pharmaceuticals. The results showed a high number of false identifications. In addition, manual processing of the data was considered laborious and ineffective. Finally, the posttarget analysis was applied to a real wastewater sample. The analysis revealed the presence of six compounds that were afterwards confirmed with standard compounds as being correct. Three psycholeptics (nordiazepam, oxazepam and temazepam) could be tentatively identified, using the identification process developed. Posttarget analysis with UPLC‐TOF‐MS proved to be a promising method for analysing wastewater samples, while we concluded that the software for nontarget analysis will need improvement before it can be used in environmental analytical work with LC‐TOF‐MS systems. Copyright © 2012 John Wiley & Sons, Ltd.     

GC–MS/MS method for the quantification of α‐cedrene in rat plasma and its pharmacokinetic application

α‐Cedrene is a pharmacologically active ingredient isolated from the essential oil of cedar. A selective and sensitive GC–MS/MS method was developed for the quantification of α‐cedrene in rat plasma for the first time. α‐Cedrene was extracted from rat plasma using ethyl acetate at neutral pH. The analytes were determined in selective reaction monitoring mode using MS/MS: m/z 204.3→119.0 for α‐cedrene and m/z 146.0→111.0 for 1,4‐dichlorobenzene (internal standard). The standard curve was linear (r² ≥ 0.995) over the concentration ranges of 5–800 ng/mL. The lower limit of quantification was 5 ng/mL using 50 μL of rat plasma. The coefficient of variation and relative error for intra‐ and interassays at four quality control levels were 3.1–13.9% and ?4.0–2.6%, respectively. The stability of processing (freeze–thaw, long‐term storage at ?80°C, and short‐term storage at room temperature) and chromatography (reinjection) was shown to be of insignificant effect. The present method was applied successfully to the pharmacokinetic study of α‐cedrene after its intravenous (10 mg/kg) and oral (25 mg/kg) administration in male Sprague‐Dawley rats.     

Nanogel engineering for new nanobiomaterials: from chaperoning engineering to biomedical applications

Nanosize hydrogels (nanogels) are polymer nanoparticles with three‐dimensional networks, formed by chemical and/or physical cross‐linking of polymer chains. Recently, various nanogels have been designed, with a particular focus on biomedical applications. In this review, we describe recent progress in the synthesis of nanogels and nanogel‐integrated hydrogels (nanogel cross‐linked gels) for drug‐delivery systems (DDS), regenerative medicine, and bioimaging. We also discuss chaperone‐like functions of physical cross‐linking nanogel (chaperoning engineering) and organic‐inorganic hybrid nanogels. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.201000008     

A biuret‐derived,MS‐cleavable cross‐linking reagent for protein structural analysis: A proof‐of‐principle study

Chemical cross‐linking combined with mass spectrometry (XL‐MS) and computational modeling has evolved as an alternative method to derive protein 3D structures and to map protein interaction networks. Special focus has been laid recently on the development and application of cross‐linkers that are cleavable by collisional activation as they yield distinct signatures in tandem mass spectra. Building on our experiences with cross‐linkers containing an MS‐labile urea group, we now present the biuret‐based, CID‐MS/MS‐cleavable cross‐linker imidodicarbonyl diimidazole (IDDI) and demonstrate its applicability for protein cross‐linking studies based on the four model peptides angiotensin II, MRFA, substance P, and thymopentin.     

A high‐throughput UHPLC–MS/MS method for the quantification of five aged butyrylcholinesterase biomarkers from human exposure to organophosphorus nerve agents

Organophosphorus nerve agents (OPNAs) are toxic compounds that are classified as prohibited Schedule 1 chemical weapons. In the body, OPNAs bind to butyrylcholinesterase (BChE) to form nerve agent adducts (OPNA–BChE). OPNA–BChE adducts can provide a reliable, long‐term protein biomarker for assessing human exposure. A major challenge facing OPNA–BChE detection is hydrolysis (aging), which can continue to occur after a clinical specimen has been collected. During aging, the o ‐alkyl phosphoester bond hydrolyzes, and the specific identity of the nerve agent is lost. To better identify OPNA exposure events, a high‐throughput method for the detection of five aged OPNA–BChE adducts was developed. This is the first diagnostic panel to allow for the simultaneous quantification of any Chemical Weapons Convention Schedule 1 OPNA by measuring the aged adducts methyl phosphonate, ethyl phosphonate, propyl phosphonate, ethyl phosphoryl, phosphoryl and unadducted BChE. The calibration range for all analytes is 2.00–250. ng/mL, which is consistent with similar methodologies used to detect unaged OPNA–BChE adducts. Each analytical run is 3 min, making the time to first unknown results, including calibration curve and quality controls, less than 1 h. Analysis of commercially purchased individual serum samples demonstrated no potential interferences with detection of aged OPNA–BChE adducts, and quantitative measurements of endogenous levels of BChE were similar to those previously reported in other OPNA–BChE adduct assays.     

A novel bioanalytical method based on UHPLC‐HRMS/MS for the quantification of oleuropein in human serum. Application to a pharmacokinetic study

A highly sensitive, rapid and specific ultrahigh‐performance liquid chromatography, coupled to negative electrospray ionization high‐resolution tandem mass spectrometry, method was developed and validated in order to investigate the absorption of dietary oleuropein (OE) in human subjects. Serum samples were collected at predefined time points, after oral administration of an olive leaf extract enriched in OE (204.4 mg OE per capsule) to two subjects. Subsequently, samples were analyzed by the developed method after a simple solid‐phase extraction step. Chromatographic separation was operated with aqueous formic acid, 0.1% (v/v), and acetonitrile following a gradient program at a flow rate of 0.45 mL/min in an RP‐C₁₈ (50 × 2.1 mm, 1.9 μm) column with a total run time of 2.7 min. The method was validated and successfully applied to the determination of OE in human serum, with the pharmacokinetic analysis of the data revealing a biphasic response.     

Orbitrap™ monostage MS versus hybrid linear ion trap MS: application to multi‐allergen screening in wine

Food allergen research has made giant steps in the last years thanks to the features offered by the latest technology of mass analyzers placed on the market allowing multiplex sensitive detection of proteins. Potentials and features of two mass analyzers namely a linear ion trap capable of performing a data dependent or selected reaction monitoring analysis and an Orbitrap^TM stand‐alone MS enabling a broadband fragmentation without mass selection at highest mass resolving power are herein described and applied to the multiplex screening of allergens in a type of wine chosen as a reference matrix. Quantitative and confirmative capabilities of both platforms were assessed on the specific case study, the multiple detection of egg and milk ‐related proteins, typically employed in white wines as fining agents. Commercial bioinformatic tools used for a quick allergen identification will be also discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

HPLC–MS/MS determination of flavonoids in Gleditsiae Spina for its quality assessment

Gleditsiae Spina, the thorn of Gleditsia sinensis Lam., has been used as an anti‐inflammatory, anti‐tumor, and anti‐bacterial traditional medicine for hundreds of years in China. This study used high‐performance liquid chromatography and tandem mass spectrometry combined with chemometric methods to allow the fast and accurate identification and quantification of the flavonoids compounds in Gleditsiae Spina, and created reliable criteria for accurate identification of Gleditsiae Spina and its adulterants. This research provides good evidence for the classification and quality evaluation of Gleditsiae Spina. Firstly, eight flavonoids compounds were detected and identified on the basis of their mass spectra, fragment characteristics, and comparison with published data. Then the mass spectroscopic fragmentation pathways of these compounds were determined and, in addition rutin, isoquercitrin, and quercitrin were detected in Gleditsiae Spina for the first time. The quantification was performed on a triple quadrupole tandem mass spectrometer in multi‐reaction monitoring mode, and the baseline separation of the eight bioactive flavonoids components was achieved within 13 min. Furthermore, the proposed method was successfully applied for simultaneous quantitative determination of the eight Gleditsiae Spina compounds and adulterants obtained from different sources in China. Then, we built a classification model which showed a high level of accuracy predicting 100% of the samples, correctly.     

The role of sample preparation in multidimensional gas chromatographic separations for non‐targeted analysis with the focus on recent biomedical,food, and plant applications

In this review, we consider and discuss the affinity and complementarity between a generic sample preparation technique and the comprehensive two‐dimensional gas chromatography process. From the initial technical development focus (e.g., on the GC×GC and solid‐phase microextraction techniques), the trend is inevitably shifting toward more applied challenges, and therefore, the preparation of the sample should be carefully considered in any GC×GC separation for an overreaching research. We highlight recent biomedical, food, and plant applications (2016–July 2020), and specifically those in which the combination of tailored sample preparation methods and GC×GC–MS has proven to be beneficial in the challenging aspects of non‐targeted analysis. Specifically on the sample preparation, we report on gas‐phase, solid‐phase, and liquid‐phase extractions, and derivatization procedures that have been used to extract and prepare volatile and semi‐volatile metabolites for the successive GC×GC analysis. Moreover, we also present a milestone section reporting the early works that pioneered the combination of sample preparation techniques with GC×GC for non‐targeted analysis.     

Chemical constituents of Meconopsis horridula and their simultaneous quantification by high‐performance liquid chromatography coupled with tandem mass spectrometry

Meconopsis horridula Hook.f. Thoms has been used as a traditional Tibetan medicine to clear away heat, relieve pain, and mobilize static blood. In this study, a reliable method based on high‐performance liquid chromatography with diode array detection and electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry was established for the identification of components in this herb. A total of 40 compounds (including 17 flavonoids, 15 alkaloids, and eight phenylpropanoids) were identified or tentatively identified. Among them, 17 components were identified in the herb for the first time. Compound 39 appears to be a novel compound, which is confirmed as 3‐(kaempferol‐8‐yl)‐2,3‐epoxyflavanone by NMR spectroscopy and mass spectrometry. Moreover, seven major constituents were simultaneously quantified by the developed high‐performance liquid chromatography with tandem triple‐quadrupole mass spectrometry method. The quantitative method was validated and quality parameters were established. The study provides a comprehensive approach for understanding this herbal medicine.