The use of ammonium formate as a mobile-phase modifier for LC-MS/MS analysis of tryptic digests

Chemical Isotope Labeling and Dual-Filtering Strategy for Comprehensive Profiling of Urinary Glucuronide Conjugates

Glucuronidation, a crucial process in phase II metabolism, plays a vital role in the detoxification and elimination of endogenous substances and xenobiotics. A comprehensive and confident profiling of glucuronate-conjugated metabolites is imperative to understanding their roles in physiological and pathological processes. In this study, a chemical isotope labeling and dual-filtering strategy was developed for global profiling of glucuronide metabolites in biological samples. N,N-Dimethyl ethylenediamine (DMED-d0) and its deuterated counterpart DMED-d6 were used to label carboxylic acids through an amidation reaction. First, carboxyl-containing compounds were extracted based on a characteristic mass difference (Δm/z, 6.037 Da) observed in MS between light- and heavy-labeled metabolites (filter I). Subsequently, within the pool of carboxyl-containing compounds, glucuronides were identified using two pairs of diagnostic ions (m/z 247.1294/253.1665 and 229.1188/235.1559 for DMED-d0/DMED-d6-labeled glucuronides) originating from the fragmentation of the derivatized glucuronic acid group in MS/MS (filter II). Compared with non-derivatization, DEMD labeling significantly enhanced the detection sensitivity of glucuronides, as evidenced by a 3- to 55-fold decrease in limits of detection for representative standards. The strategy was applied to profiling glucuronide metabolites in urine samples from colorectal cancer (CRC) patients. A total of 685 features were screened as potential glucuronides, among which 181 were annotated, mainly including glucuronides derived from lipids, organic oxygen, and phenylpropanoids. Enzymatic biosynthesis was employed to accurately identify unknown glucuronides without standards, demonstrating the reliability of the dual-filtering strategy. Our strategy exhibits great potential for profiling the glucuronide metabolome with high coverage and confidence to reveal changes in CRC and other diseases.

Emerging contaminants as unintentional substances in paper and board: A case of unexpected pharmaceuticals detection in the paper recycling chain

The contamination of paper products by various chemicals has been reported on a global level, but to date, no published research has investigated pharmaceutical contamination of paper-based products. In this study, pharmaceutical analysis was conducted on 42 samples collected from various points of the recycled paper value chain in Cape Town, South Africa, which included the various grades that may be included in the manufacturing of recycled paperboard. The analysis was achieved by ultrasonic-assisted extraction of paper samples before detection by UHPLC-Q Orbitrap. Quantification limits ranged from 1.15 pg/g for ketoprofen to 46.07 pg/g for methocarbamol. Pharmaceuticals identified in newspaper samples were dexamethasone, ketoprofen, and 17β-estradiol. The latter was also detected in paper shopping bags (up to 697.49 ng/g), infant bathtub packaging (280.62 ng/g), battery packaging (137.43 ng/g), and an egg carton (170.47 ng/g). Carbamazepine was also prominent with its concentration reaching 13.02 ng/g in a vegetable box. Suspect screening tentatively identified 14 additional pharmaceuticals in paper samples, with minocycline, prazepam, and anabolic steroids appearing more prominently. This pioneering study indicated that unintentional pharmaceutical exposure had expanded beyond environmental media to consumer products.

Comprehensive two-dimensional liquid chromatography with high resolution mass spectrometry to investigate the photoelectrochemical degradation of environmentally relevant pharmaceuticals and their degradation products in water

The widespread presence of organic micropollutants in the environment reflects the inability of traditional wastewater treatment plants to remove them. In this context, advanced oxidation processes (AOPs) have emerged as promising quaternary wastewater treatment technologies since they efficiently degrade recalcitrant components by generating highly reactive free radicals. Nonetheless, the chemical characterization of potentially harmful byproducts is essential to avoid the contamination of natural water bodies with hazardous substances. Given the complexity of wastewater matrices, the implementation of comprehensive analytical methodologies is required. In this work, the simultaneous photoelectrochemical degradation of seven environmentally relevant pharmaceuticals and one metabolite from the EU Watch List 2020/1161 was examined in ultrapure water and simulated wastewater, achieving excellent removal efficiencies (overall >95%) after 180 min treatment. The reactor unit was linked to an online LC sample manager, allowing for automated sampling every 15 min and near real-time process monitoring. Online comprehensive two-dimensional liquid chromatography (LC × LC) coupled with high resolution mass spectrometry (HRMS) was subsequently used to tentatively identify degradation products after photoelectrochemical degradation. Two reversed-phase liquid chromatography (RPLC) columns were used: an SB-C18 column operated with 5 mM ammonium formate at pH 5.8 (1A) and methanol (1B) as the mobile phases in the first dimension and an SB-Aq column using acidified water at pH 3.1 (2A) and acetonitrile (2B) as the mobile phases in the second dimension. This resulted in a five-fold increase in peak capacity compared to one-dimensional LC while maintaining the same total analysis time of 50 min. The LC x LC method allowed the tentative identification of 12 venlafaxine, 7 trimethoprim and 10 ciprofloxacin intermediates. Subsequent toxicity predictions suggested that some of these byproducts were potentially harmful. This study presents an effective hybrid technology for the simultaneous removal of pharmaceuticals from contaminated wastewater matrices and demonstrates how multidimensional liquid chromatography techniques can be applied to better understand the degradation mechanisms after the treatment of micropollutants with AOPs.

Expanding the structural resolution of glycosylation microheterogeneity in therapeutic proteins by salt-free hydrophilic interaction liquid chromatography tandem mass spectrometry

Glycosylation affects the safety and efficacy of therapeutic proteins and is often considered a critical quality attribute (CQA). Therefore, it is important to identify and quantify glycans during drug development. Glycosylation is a highly complex post-translational modification (PTM) due to its structural heterogeneity, i.e. glycosylation site occupancy, glycan compositions, modifications, and isomers. Current analytical tools compromise either structural resolution or site specificity. Hydrophilic interaction liquid chromatography-fluorescence-mass spectrometry (HILIC-FLR-MS) is the gold standard for structural analysis of released glycans, but lacks information on site specificity and occupation. However, HILIC-FLR-MS often uses salt in the solvent, which impairs analysis robustness and sensitivity. Site-specific glycosylation analysis via glycopeptides, upon proteolytic digestion, is commonly performed by reversed-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS), but provides only compositional and limited structural glycan information. In this study, we introduce a salt-free, glycopeptide-based HILIC-tandem mass spectrometry (HILIC-MS/MS) method that provides glycan identification, glycan isomer separation and site-specific information simultaneously. Moreover, HILIC-MS/MS demonstrated comparable relative quantification results as released glycan HILIC-FLR-MS. Further, our new method improves the retention of hydrophilic peptides, allowing simultaneous analysis of important CQAs such as deamidation in antibodies. The developed method offers a valuable tool to streamline the site-specific glycosylation analysis of glycoproteins, which is particularly important for the expanding landscape of novel therapeutic formats in the biopharmaceutical industry.

A Novel Multi-ion Evaluation Scheme to Determine Stable Chlorine Isotope Ratios (37Cl/35Cl) of Chlordecone by LC-QTOF

Organochlorinated pesticides are highly persistent organic pollutants having important adverse effects in the environment. To study their fate, compound-specific isotope analysis (CSIA) may be used to investigate their degradation pathways and mechanisms but is currently limited to 13C isotope ratios. The assessment of 37Cl isotope ratios from mass spectra is complicated by the large number of isotopologues of polychlorinated compounds. For method development, chlordecone (C10Cl10O2H2; hydrate form), an organochlorine insecticide that led to severe contamination of soils and aquatic ecosystems of the French West Indies, was taken as a model analyte. Chlorine isotope analysis of chlordecone hydrate was evaluated using high-resolution liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS), enabling smooth ionization to detect the molecular ion. First, a new evaluation scheme is presented to correct for multiple isotope presence in polychlorinated compounds. The scheme is based on probability calculations of the most frequent isotopologues, distributions by binomial probability functions, and corrections for the presence of nonchlorine heavy isotopes. Second, mobile-phase modifiers, ionization energy (sampling cone tension) and scan time were optimized for accurate chlorine isotope ratios. Chlordecone standard samples were measured up to 10-fold and bracketed with a second chlordecone external standard. δ37Cl values were obtained after conversion to the SMOC scale by a two-point calibration. The robustness of the analysis method and evaluation scheme were tested and gave satisfactory results with standard errors (σm) of ±0.34‰ for precision and ±0.89‰ for long-term accuracy of chlorine isotope ratios of chlordecone hydrate. This work opens perspectives for applications of the C-Cl CSIA approach to investigate the fate of highly toxic and low reactive polychlorinated compounds in the environment.

Chiral separation of racemic closantel and ultratrace detection of its enantiomers in bacteria by enhanced liquid chromatography-tandem mass spectrometry combined with postcolumn infusion of ammonia

Reliable analysis of ultratrace antibiotics in bacterial cells may become a new means to elucidate the antibacterial mechanism, drug resistance and environmental fate. In this work, an ultrahigh-sensitive, accurate and enhanced liquid chromatography-tandem mass spectrometric method was first developed for chiral separation and detection of racemic closantel, as an antibacterial adjuvant. Optimizing acetonitrile-water-formic acid system that is compatible with mass spectrometry as a mobile phase, the baseline separation of two enantiomers was achieved by using EnantioPak® Y1-R chiral column, and the resolution of the two analytes was more than 1.95. Further adopt the strategy of postcolumn infusion of ammonia, the mobile phase pH was reversed from acidic condition suitable for the optimal chromatographic separation of R- and S-closantel to alkaline, so that closantel could realize efficient electrospray ionization under the preferred negative ion mode. The bacterial cells were subjected to be frozen-cracked, and the analytes were extracted with acetonitrile after clipping the pointed bottom of the Eppendorf tube into a new tube. The method was linear over concentration ranges of 0.5-50 pg/mL (r²≥0.99) for R- and S-closantel. The detection limits of target analytes were all 0.15 pg/mL in bacterial cells. The average recoveries of two enantiomers ranged from 81.2% to 107.8% with relative standard deviations below 15%. The method proposed might be important support for the deep research of the stereoselectivity of biological activity, toxicity and metabolism of closantel enantiomers.

Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.

Surface-Charged Hybrid Monolithic Column for MS-Compatible Peptide Separation with High Peak Capacity and Its Application in Proteomic Analysis

For bottom-up proteomics, peptide separation with high peak capacity under MS-compatible conditions is of vital significance to increase proteome coverage. Herein, a surface-charged ethane-bridged hybrid monolithic column was prepared based on the efficient ring-opening reaction of N-methyl-aza-2,2,4-trimethyl-silacyclopentane after C18-functionalization. The existence of secondary amino groups on the surface was beneficial to reduce the secondary interactions of silanol groups and increase peak capacity for peptide separation with MS-compatible mobile phases (e.g., using 0.1% FA as the mobile phase modifier). Such columns offered a 4-fold increase in peak capacity compared with ethane-bridged hybrid monolithic columns without surface charge modification. By a 100 cm length surface-charged ethane-bridged hybrid capillary column, high peak capacity of 700 was achieved within a 240 min gradient for the separation of Hela tryptic peptides with 0.1% FA-containing mobile phases, under the low backpressure of ∼200 bar. On average, 44493 ± 459 peptides corresponding to 5148 ± 47 proteins were identified from 750 ng Hela tryptic digests. Finally, the surface-charged ethane-bridged hybrid monolithic column was successfully applied in the quantitative proteomic analysis of dopaminergic neuron death model of N-methyl-4-phenylpyridinium iodide induced SH-SY5Y cells. These results demonstrated great promise of such surface-charged ethane-bridged hybrid monolithic columns for bottom-up proteomic analysis in complex samples.

Proteomic profiling in extracellular vesicles for cancer detection and monitoring

Extracellular vesicles (EVs) are nanometer-size lipid vesicles released by cells, which play essential biological functions in intercellular communication. Increasing evidence indicates that EVs participate in cancer development, including invasion, migration, metastasis, and cancer immune modulation. One of the key mechanisms is that EVs affect different cells in the tumor microenvironment through surface-anchor proteins and protein cargos. Moreover, proteins specifically expressed in tumor-derived EVs can be applied in cancer diagnosis and monitoring. Besides, the EV proteome also helps to understand drug resistance in cancers and to guide clinical medication. With the development of mass spectrometry and array-based multi-protein detection, the research of EV proteomics has entered a new era. The high-throughput parallel proteomic profiling based on these new platforms allows us to study the impact of EV proteome on cancer progression more comprehensively and to describe the proteomic landscape in cancers with more details. In this article, we review the role and function of different types of EVs in cancer progression. More importantly, we summarize the proteomic profiling of EVs based on different methods and the application of EV proteome in cancer detection and monitoring.

Dispersive Liquid-Liquid Microextraction (DLLME) and LC-MS/MS Analysis for Multi-Mycotoxin in Rice Bran: Method Development, Optimization and Validation

Rice bran, a by-product of the rice milling process, has emerged as a functional food and being used in formulation of healthy food and drinks. However, rice bran is often contaminated with numerous mycotoxins. In this study, a method to simultaneous detection of aflatoxins (AFB1, AFB2, AFG1, and AFG2), ochratoxin A (OTA), deoxynivalenol (DON), fumonisins (FB1 and FB2), sterigmatocystin (STG), T-2 toxin, HT-2 toxin, diacetoxyscirpenol (DAS) and zearalenone (ZEA) in rice bran was developed, optimized and validated using dispersive liquid–liquid microextraction (DLLME) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). In DLLME, using a solvent mixture of methanol/water (80:20, v/v) as the dispersive solvent and chloroform as the extraction solvent with the addition of 5% salt improved the extraction recoveries (63–120%). The developed method was further optimized using the response surface methodology (RSM) combined with Box–Behnken Design (BBD). Under the optimized experimental conditions, good linearity was obtained with a correlation coefficient (r²) ≥ 0.990 and a limit of detection (LOD) between 0.5 to 50 ng g⁻¹. The recoveries ranged from 70.2% to 99.4% with an RSD below 1.28%. The proposed method was successfully applied to analyze multi-mycotoxin in 24 rice bran samples.

Investigation into reversed-phase chromatography peptide separation systems Part IV: Characterisation of mobile phase selectivity differences

The differentiation of mobile phase compositions between sub-classes which exhibit distinct chromatographic selectivity (i.e. termed characterisation) towards a range of peptide probes with diverse functionality and hence the possibility for multi-modal retention mechanisms has been undertaken. Due to the complexity of peptide retention mechanisms in given mobile phase conditions, no attempt has been made to explain these, instead mobile phases have simply been classified into distinct groups with an aim of identifying those yielding differing selectivities for use in strategic method development roadmaps for the analysis of peptide mixtures. The selectivity differences between nine synthetic peptides (fragments of [Ile27]-Bovine GLP-2) were used to assess how fifty-one RPC mobile phase compositions of differing pH (range 1.8 - 7.8), salt types, ionic strengths, ion-pair reagents and chaotropic / kosmotropic additives affected chromatographic selectivity on a new generation C18 stationary phase (Ascentis Express C18). The mobile phase compositions consisted of commonly used and novel UV or MS compatible additives. The chemometric tool of Principal Component Analysis (PCA) was used to visualise the differences in selectivity generated between the various mobile phases evaluated. The results highlight the importance of screening numerous mobile phases of differing pH, ion-pair reagents and ionic strength in order to maximise the probability of achieving separation of all the peptides of interest within a complex mixture. PCA permitted a ranking of the relative importance of the various mobile phase parameters evaluated. The concept of using this approach was proven in the analysis of a sample of Bovine GLP-2 (1-15) containing synthesis related impurities. Mobile phases with high ionic strength were demonstrated to be crucial for the generation of symmetrical peaks. The observations made on the C18 phase were compared on three additional stationary phases (i.e. alkyl amide, fluorophenyl and biphenyl), which had previously been shown to possess large selectivity differences towards these peptides, on a limited sub-set of mobile phases. With the exception of the ion-pair reagent, similar trends were obtained for the C18, fluorophenyl and biphenyl phases intimating the applicability of these findings to the vast majority of RPC columns (i.e. neutral or weakly polar in character) which are suitable for the analysis of peptides. The conclusions were not relevant for columns with a more disparate nature (i.e. containing a high degree of positive charge).

Simultaneous Analysis of Fenthion and Its Five Metabolites in Produce Using Ultra-High Performance Liquid Chromatography-Tandem Mass Spectrometry

A simultaneous analytical method for the organophosphorus insecticide fenthion and its five metabolites (fenthion oxon, fenthion oxon sulfoxide, fenthion oxon sulfone, fenthion sulfoxide, and fenthion sulfone) was developed based on ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Five matrices (brown rice, chili pepper, orange, potato, and soybean) were selected to validate the method. The target compounds were analyzed using positive electrospray ionization in the multiple reaction monitoring mode. For the best sensitivity in regard to the detector response, water and methanol containing formic acid (0.1%) were selected as the mobile phase. The optimum extraction efficiency was obtained through a citrate-buffered QuEChERS (quick, easy, cheap, effective, rugged, and safe) method. Recovery tests were carried out at three spiking levels (n = 3). At all fortification levels, the accuracy and precision results were between 70% and 120% with a relative standard deviation of ≤15%. The limit of quantitation was 0.01 mg/kg, and the correlation coefficients (r²) of the matrix-matched calibration curves were >0.99. Significant signal suppression in the detector responses were observed for all matrices, suggesting that a compensation method, such as matrix-matched calibration, is required to provide accurate quantitative results. The applicability of the presented method was confirmed for the simultaneous analysis of fenthion and its metabolites in various crops.

Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control

Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along with the sample preparation protocol, in particular, after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in the MS-loading solvent, consuming only 2 μL of sample. We compared the performance of the microfluidic spectrophotometer with a standard device and determined the optimal sample amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. A careful evaluation of selected LC and MS parameters allowed us to define 3 μg as an optimal peptide amount to be injected into this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells and showing that injecting equal peptide amounts, rather than approximate ones, result in less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control.

HILIC-MRM-MS for Linkage-Specific Separation of Sialylated Glycopeptides to Quantify Prostate-Specific Antigen Proteoforms

Elevated serum prostate-specific antigen (PSA) levels in body fluids may indicate prostate cancer (PCa), but it is noted that the clinical performance is rather poor. Specificity and sensitivity values of 20 and 94% at a cutoff value of 4.1 ng/mL, respectively, result in overdiagnosis and unnecessary interventions. Previous exploratory studies have indicated that the glycosylation of PSA potentially leads to improved PCa diagnosis based on qualitative analyses. However, the applied methods are not suited for a quantitative evaluation or implementation in a medical laboratory. Therefore, in this proof-of-principle study, we have evaluated the use of hydrophilic interaction liquid chromatography (HILIC) in combination with targeted quantitative mass spectrometry for the sialic acid linkage-specific analysis of PSA glyco-proteoforms based on either trypsin or ArgC peptides. The efficiency of PSA proteolysis was optimized as well as the glycopeptide separation conditions (buffer type, strength, and pH). The HILIC-based analysis of PSA glyco-proteoforms presented here has the potential for the clinical validation of patient cohorts. The method shows the feasibility of the use of a HILIC stationary phase for the separation of isomeric glycopeptides to detect specific glyco-proteoforms. This is the first step toward the development and evaluation of PSA glyco-proteoforms for use in a clinical chemistry setting aiming for improved PCa diagnosis or screening.

Bioanalytical method development and validation for determination of fibroblast growth factor peptide and its application to pharmacokinetic studies

Fibroblast growth factor peptide (FGF-P) is a polypeptide analog of FGF-2 that could be a potential mitigation and treatment agent for radiation syndromes. Prior to conducting preclinical pharmacokinetics, we developed and validated the LC-MS/MS bioanalytical method for determination of FGF-P in rat plasma for the first time. FGF-P was extracted from rat plasma using the protein precipitation technique followed liquid-liquid extraction using dichloromethane as a solvent. The mobile phases consisted of two components: (a) 0.1% formic acid in water; and (b) acetonitrile: 0.1% formic acid in water (95:5) under gradient elution. The validated method was also successfully applied to a pharmacokinetic study of FGF-P (10 mg/kg, intravenous) in Wistar rats. The method proved to be specific, accurate, precise, and linear over the concentration range of 2-500 ng/mL with coefficient of determination greater than 0.99 in all validation batches. The within-run and between-run accuracy was 87.97-115.00% with a precision of less than 14%. The mean recoveries ranged from 88.14% to 101.73%. The stability of the compound in plasma samples was proven under various storage conditions. After intravenous administration of FGF-P (10 mg/kg) the C₀ was 70.4 µg/mL and the AUC was 86.2 µg*min/mL.

Recent update on methodologies for extraction and analysis of soybean seed proteins

Soybean is one of the best sources of plant protein. Development of improved soybean cultivars through classical breeding and new biotech approaches is important to meet the growing global demand for soybeans. There is a critical need to investigate changes in protein content and profiles to ensure the safety and nutritional quality of new soybean varieties and their food products. A proteomics study begins with an optimal combination of extraction, separation and detection approaches. This review attempts to provide a summary of current updates in the methodologies used for extraction, separation and detection of protein from soybean, the basic foundations for good proteomic research. This information can be effectively used to investigate modifications in protein content and profiles in new varieties of soybeans and other crops. © 2018 Society of Chemical Industry.

Development of a reversed phase liquid chromatographic method for analysis of pyridoxal-5'-phosphate and its impurities

Since no proper method is available in literature for the analysis of pyridoxal-5'-phosphate, a reversed phase liquid chromatographic method was developed and validated for specificity, sensitivity, linearity, precision and accuracy. Nine potential related substances and forced degradation products could be successfully separated from the main peak. The separation was achieved on a Polaris C18 column (250 × 4.6 mm i.d., 5 μm) using a mobile phase consisting of 20 mM ammonium formate in 0.65% formic acid - acetonitrile (98.8:1.2, v/v). Isocratic elution was performed at a flow rate of 1.0 mL/min and the analytes were detected by UV at 240 nm. The volatile mobile phase allowed also direct coupling to an ion-trap mass spectrometer with a positive electrospray ionization source to characterize unknown peaks in the chromatogram. The method can be used for quality control purposes as required by regulatory authorities to ensure the product's safety and efficacy.

Structure determination of disease associated peak AAA from l-Tryptophan implicated in the eosinophilia-myalgia syndrome

The eosinophilia-myalgia syndrome (EMS) outbreak of 1989 that occurred in the USA and elsewhere was caused by the ingestion of l-Tryptophan (L-Trp) solely manufactured by the Japanese company Showa Denko K.K. (SD). Six compounds present in the SD L-Trp were reported to be case-associated contaminants. However, "one" of these compounds, Peak AAA has remained structurally uncharacterized, despite the fact that it was described as "the only statistically significant (p=0.0014) contaminant". Here, we employ on-line microcapillary-high performance liquid chromatography-electrospray ionization mass spectrometry (LC-MS), and tandem mass spectrometry (MS/MS) to determine that Peak AAA is in fact two structurally related isomers. Peak AAA₁ and Peak AAA₂ differed in LC retention times, and were determined by accurate mass-LC-MS to both have a protonated molecular ion (MH⁺⁾ of mass 343.239Da (Da), corresponding to a molecular formula of C₂₁H₃₀N₂O_2, and possessing eight degrees of unsaturation (DoU) for the non-protonated molecule. By comparing the LC-MS and LC-MS-MS retention times and spectra with authentic synthetic standards, Peak AAA₁ was identified as the intermolecular condensation product of L-Trp with anteiso 7-methylnonanoic acid, to afford (S)-2-amino-3-(2-((S,E)-7-methylnon-1-en-1-yl)-1H-indol-3-yl)propanoic acid. Peak AAA₂ was determined to be a condensation product of L-Trp with decanoic acid, which produced (S)-2-amino-3-(2-((E)-dec-1-en-1-yl)-1H-indol-3-yl)propanoic acid.

A rapid and sensitive liquid chromatography-tandem mass spectrometric method for the determination of hederasaponin B in rat plasma: Application to a pharmacokinetic study

A rapid, simple and sensitive ultra-high performance liquid chromatography-tandem mass spectrometric (UPLC-MS/MS) method was developed and validated for the determination of hederasaponin B, an active triterpenoid saponin widely existed in Hedera helix L. Plasma samples were processed by protein precipitation with acetonitrile and separated on a Thermo Hypersil GOLD C₁₈ (2.1 mm × 50 mm,1.9 µm) at flow rate of 0.3 ml/min, with a gradient elution consisting of acetonitrile and water containing 0.1% (v/v) formic acid at 30 °C and detected by electrospray ionization mass spectrometry in the positive multiple reaction monitoring (MRM) mode. The linearity was found to be within the concentration range of 0.5-5000 ng/ml with a lower limit of quantification of 0.5 ng/ml. The absolute oral bioavailability of hederasaponin B was 0.24 ± 0.49%. This indicated that the concentration-time course of the hederasaponin B existed a double-peak phenomenon. This method was further applied to the determination of hederasaponin B in rat plasma and showed good practicability, for the first time, after intragastric (25 mg/kg) and intravenous (2 mg/kg) administration in rats.

Column switching UHPLC–MS/MS with restricted access material for the determination of CNS drugs in plasma samples

Background: Polypharmacy is a common practice in schizophrenia. Consequently, therapeutic drug monitoring is usually adopted to maintain the concentrations of the drugs in the plasma within a targeted therapeutic range, to maximize therapeutic efficiency and to diminish adverse side effects. Methodology: This study reports on a column switching UHPLC–MS/MS method to determine psychotropic drugs in plasma samples simultaneously. Results: The method was linear from 0.025 to 1.25 ng ml-1 with R2 above 0.9950 and the lack of fit test (p > 0.05). The precision values presented coefficients of variation lower than 12%, and the relative standard error of the accuracy were lower than 14%. Conclusion: The column switching UHPLC–MS/MS method developed herein successfully determined drugs in schizophrenic patients’ plasma samples for therapeutic drug monitoring.

Pharmacokinetic parameters of three active ingredients hederacoside C, hederacoside D, and ɑ-hederin in Hedera helix in rats

In Hedera helix hederacoside C, hederacoside D, and ɑ-hederin are three major bioactive saponins and play pivotal roles in the overall biological activity. In this study, a specific and sensitive ultra-high performance liquid chromatography with tandem mass spectrometry method has been developed and validated for the quantification of three major bioactive saponins in rat plasma. Chromatographic separation was performed on a reversed-phase Thermo Hypersil GOLD C18 column (2.1 mm × 50 mm, 1.9 μm) using a gradient mobile phase system of acetonitrile-water containing 0.1% formic acid. The assay was successfully applied to study the pharmacokinetic behavior of the three analytes in rats after oral and intravenous administration of a mixture of saponins (hederacoside C, hederacoside D, and ɑ-hederin). Further research was performed to compare the pharmacokinetic behavior of the three analytes after the oral administration of a mixture of saponins and an extract of saponins from Hedera helix, and results showed that double peaks were evident on concentration-time profile for each of the three saponins. The difference in the pharmacokinetic characteristics of three saponins between a mixture of saponins and an extract of saponins from Hedera helix was found in rat, which would be beneficial for the preclinical research and clinical use of Hedera helix.

Development, validation and application of an ultra high performance liquid chromatographic-tandem mass spectrometric method for the simultaneous detection and quantification of five different classes of veterinary antibiotics in swine manure

In this study, a fast, simple and selective ultra high performance liquid chromatographic-tandem mass spectrometric (UHPLC-MS/MS) method for the simultaneous detection and quantification of colistin, sulfadiazine, trimethoprim, doxycycline, oxytetracycline and ceftiofur and for the detection of tylosin A in swine manure was developed and validated. First, a simple extraction procedure with acetonitrile and 6% trichloroacetic acid was carried out. Second, the supernatant was evaporated and the pellet was reconstituted in 1 ml of water/acetonitrile (80/20) and 0.1% formic acid. Extracts were filtered and analyzed by UHPLC-MS/MS on a Kinetex C18 column using gradient elution. The method developed was validated according to the criteria of Commission Decision 2002/657/EC. Recovery percentages varied between 94% and 106%, repeatability percentages were within the range of 1.7-9.2% and the intralaboratory reproducibility varied between 2.8% and 9.3% for all compounds, except for tylosin A for which more variation was observed resulting in a higher measurement uncertainty. The limit of detection and limit of quantification varied between 1.1 and 20.2 and between 3.5 and 67.3 μg/kg, respectively. This method was used to determine the presence and concentration of the seven antibiotic residues in swine manure sampled from ten different manure pits on farms where the selected antibiotics were used. A link was found between the antibiotics used and detected, except for ceftiofur which is injected at low doses and degraded readily in swine manure and was therefore not recovered in any of the samples. To the best of our knowledge, this is the first method available for the simultaneous extraction and quantification of colistin with other antibiotic classes. Additionally, colistin was never extracted from swine manure before. Another innovative aspect of this method is the simultaneous detection and quantification of five different classes of antibiotic residues in swine manure.

A rapid LC–MS/MS quantification of peramivir using a simple and inexpensive sample precipitation: application to PK

Aim: Peramivir is a newly approved selective neuraminidase inhibitor designed to inhibit influenza virus infection. Methodology/results: We report a robust and sensitive method utilizing simple precipitation extraction with LC–MS/MS for the high-throughput quantification. Addition of 0.06 M of ammonium formate and 0.1% formic acid in mobile phase could help reduce the matrix effect. This method uses 100 µl of plasma and covers a linear concentration range from 5 to 10,000 ng/ml. Other validation parameters are also evaluated and meet regulatory expectations by US FDA guidelines. Conclusion: The developed HPLC–MS/MS method has been successfully applied to support a clinical pharmacokinetic study. The strategy presented here can be applied elsewhere and may be useful for other amphiphilic drugs.

The role of protein and peptide separation before mass spectrometry analysis in clinical proteomics

The purpose of clinical proteomics is to characterise protein profiles of a plethora of diseases with the aim of finding specific biomarkers. These are particularly valuable for early diagnosis, and represent key molecules suitable to elucidate pathogenic mechanisms. Samples deriving from patients (i.e. blood, urine, cerebrospinal fluid, biopsies) are the sources for clinical proteomics. Due to the complexity of the extracted samples their direct analysis is unachievable. Any analytical clinical proteomics study should start with the choice of the optimal combination of strategies with respect to both sample preparations and MS approaches. Protein or peptide fractionation (off-line or on-line) is essential to reduce complexity of biological samples and to achieve the most complete and reproducible analysis. The aim of this review is to introduce the readers to a functional range of strategies to help scientists in their proteomics set up. In particular, the separation approaches of proteins or peptides (both gel-based and gel-free) are reviewed with special attention paid to their advantages and limitations, and to the different liquid chromatography techniques used to peptide fractionation after protein enzymatic digestion and before their detection. Finally, the role of mass spectrometry (MS) for protein identification and quantification is discussed including emerging MS data acquisition strategies.

Advances in LC-MS/MS-based glycoproteomics: getting closer to system-wide site-specific mapping of the N- and O-glycoproteome

Site-specific structural characterization of glycoproteins is important for understanding the exact functional relevance of protein glycosylation. Resulting partly from the multiple layers of structural complexity of the attached glycans, the system-wide site-specific characterization of protein glycosylation, defined as glycoproteomics, is still far from trivial leaving the N- and O-linked glycoproteomes significantly under-defined. However, recent years have seen significant advances in glycoproteomics driven, in part, by the developments of dedicated workflows and efficient sample preparation, including glycopeptide enrichment and prefractionation. In addition, glycoproteomics has benefitted from the continuous performance enhancement and more intelligent use of liquid chromatography and tandem mass spectrometry (LC-MS/MS) instrumentation and a wider selection of specialized software tackling the unique challenges of glycoproteomics data. Together these advances promise more streamlined N- and O-linked glycoproteome analysis. Tangible examples include system-wide glycoproteomics studies detecting thousands of intact glycopeptides from hundreds of glycoproteins from diverse biological samples. With a strict focus on the system-wide site-specific analysis of protein N- and O-linked glycosylation, we review the recent advances in LC-MS/MS based glycoproteomics. The review opens with a more general discussion of experimental designs in glycoproteomics and sample preparation prior to LC-MS/MS based data acquisition. Although many challenges still remain, it becomes clear that glycoproteomics, one of the last frontiers in proteomics, is gradually maturing enabling a wider spectrum of researchers to access this new emerging research discipline. The next milestone in analytical glycobiology is being reached allowing the glycoscientist to address the functional importance of protein glycosylation in a system-wide yet protein-specific manner.

Optimized superficially porous particles for protein separations

Continuing interest in larger therapeutic molecules by pharmaceutical and biotech companies provides the need for improved tools for examining these molecules both during the discovery phase and later during quality control. To meet this need, larger pore superficially porous particles with appropriate surface properties (Fused-Core(®) particles) have been developed with a pore size of 400 Å, allowing large molecules (<500 kDa) unrestricted access to the bonded phase. In addition, a particle size (3.4 μm) is employed that allows high-efficiency, low-pressure separations suitable for potentially pressure-sensitive proteins. A study of the shell thickness of the new fused-core particles suggests a compromise between a short diffusion path and high efficiency versus adequate retention and mass load tolerance. In addition, superior performance for the reversed-phase separation of proteins requires that specific design properties for the bonded-phase should be incorporated. As a result, columns of the new particles with unique bonded phases show excellent stability and high compatibility with mass spectrometry-suitable mobile phases. This report includes fast separations of intact protein mixtures, as well as examples of very high-resolution separations of larger monoclonal antibody materials and associated variants. Investigations of protein recovery, sample loading and dynamic range for analysis are shown. The advantages of these new 400 Å fused-core particles, specifically designed for protein analysis, over traditional particles for protein separations are demonstrated.