Urine sample preparation for proteomic analysis

Sample preparation for both environmental and more importantly biological matrices is a bottleneck of all kinds of analytical processes. In the case of proteomic analysis this element is even more important due to the amount of cross‐reactions that should be taken into consideration. The incorporation of new post‐translational modifications, protein hydrolysis, or even its degradation is possible as side effects of proteins sample processing. If protocols are evaluated appropriately, then identification of such proteins does not bring difficulties. However, if structural changes are provided without sufficient attention then protein sequence coverage will be reduced or even identification of such proteins could be impossible. This review summarizes obstacles and achievements in protein sample preparation of urine for proteome analysis using different tools for mass spectrometry analysis. The main aim is to present comprehensively the idea of urine application as a valuable matrix. This article is dedicated to sample preparation and application of urine mainly in novel cancer biomarkers discovery.     

Determination of Urea in Milk by Liquid Chromatography-Isotope Dilution Mass Spectrometry

A definitive method based on liquid chromatography isotope dilution mass spectrometry (LC-IDMS) has been developed for the determination of milk urea, an indicator of nutrition status for the lactating animals. The milk samples were treated twice by sequentially adding acetonitrile and chloroform to precipitate proteins and then were directly separated using normal phase liquid chromatography without chemical derivatization. After the matrix separation, exact matching IDMS was used for the determination of milk urea, with high accuracy, high precision, good linearity and low uncertainty. The recoveries obtained for the four spiked milk samples were 100.6–102.2%. The linear range of signal responses was 10–2000 mg · kg^?1 with a linearity coefficient of 0.9995. The intraday and interday precisions in terms with relative standard deviations (RSDs) were 0.17–0.38% and 0.28–0.40%, respectively. The uncertainties of the whole sample analysis process were estimated to be 0.83%, 0.60%, and 0.64% for three samples with concentrations of 151.28, 184.36, and 266.66 mg · kg^?1.     

Evaluation of the combination of a dispersive liquid–liquid microextraction method with micellar electrokinetic chromatography coupled to mass spectrometry for the determination of estrogenic compounds in milk and yogurt

In this work, the suitability of a methodology based on dispersive liquid–liquid microextraction (DLLME) has been evaluated for the extraction of four endoestrogens (estriol, 17α‐estradiol, 17β‐estradiol, and estrone), an exoestrogen (17α‐etynylestradiol), and a mycotoxin (zearalenone), together with some of their major metabolites (2‐methoxyestradiol, α‐zearalanol, β‐zearalanol, α‐zearalenol, and β‐zearalenol) from different types of milk (whole and skimmed cow milk and semiskimmed goat milk) and whole natural yogurt. The methodology includes a previous protein precipitation with acidified ACN and a defatting step with n‐hexane. Separation of the analytes, determination, and quantification were developed by MEKC coupled to ESI‐MS using a BGE containing an aqueous solution of ammonium perfluorooctanoate as MS friendly surfactant. Calibration, precision, and accuracy studies of the described DLLME‐MEKC‐MS/MS method were evaluated obtaining a good linearity and LODs in the low micrograms per liter range.     

Determination of 16 polycyclic aromatic hydrocarbons in milk and related products using solid-phase microextraction coupled to gas chromatography-mass spectrometry

A method for the determination of 16 polycyclic aromatic hydrocarbons (PAHs) in milk and related products based on direct immersion-solid phase microextraction (DI-SPME) followed by gas chromatography-mass spectrometry detection (GC-MS) has been developed. The influence of various parameters on PAH extraction efficiency was carefully monitored. Good performance (recovery, precision and quantitation limits) was attained when a PDMS/DVB fiber was immersed in the sample for 60 min at 55 °C. Detection limits ranged from 0.003 to 1.5 μg L⁻¹ at a signal-to-noise ratio of 3, depending on the compound and the sample. The proposed method was successfully applied to infant formulas, milk and related products and the presence of both fluoranthene and pyrene in two samples was confirmed.     

Impurity Profiling of Dirithromycin by Liquid Chromatography Coupled to Electrospray Ionization Mass Spectrometry

The aim of this study was to characterize as much as possible the unknown peaks in the chromatogram obtained with a non-volatile LC-UV system, which was published earlier for the separation of dirithromycin and its related substances. For this purpose, each peak eluting from the non-volatile system was collected and transferred to a MS, after performing a desalting process. The desalting procedure uses a XTerra RP C₁₈ column (250 mm x 4.6 mm, 5 µm) and two mobile phases consisting of a mixture of water / 0.1% (v/v) formic acid and a mixture of acetonitrile / 0.1% (v/v) formic acid, respectively. Mass spectral data were acquired on an LCQ ion trap mass spectrometer equipped with an electrospray ionization source (ESI), operating in the positive ion mode. In addition to the thirteen already known compounds, seven new compounds were elucidated. Five impurities showed modifications at the amino group of the desosamine molecule, one an alteration at position C-9 and one a modification at position C-13 of the macrolide ring.     

Application of displacement chromatography for the proteome analysis of a human plasma protein fraction

It was the aim of this study to compare the performance of displacement chromatography with gradient elution chromatography both applied as the cation-exchange separation step for a proteome analysis in a bottom-up approach using multidimensional chromatography for the separation of tryptic peptides prior to their mass spectrometric analysis. The tryptic digest of the human Cohn fraction IV-4 served as a sample. For both chromatography modes commonly used operating parameters were chosen thus ensuring optimal separation results of equal sample amounts for each mode. All resulting fractions were analyzed with an HPLC-chip–LC–MS system. The eluate of the HPLC-chip column was ionized by electrospray ionization (ESI) and analyzed with an ion-trap mass spectrometer. For guaranteeing high confidence concerning the identity of the peptides, the mass spectrometric data were processed by different bioinformatic tools applying stringent criteria. By the displacement approach the total amount of identified proteins (78) was significantly higher than in the gradient mode (58). The results showed that displacement chromatography is a well suited alternative in comparison to gradient elution separation for analysis of proteomes via the bottom-up approach applying multidimensional chromatography, especially in those cases when larger quantities of proteins are available.     

Solid-phase microextraction followed by gas chromatography-mass spectrometry for the determination of ink photo-initiators in packed milk

A novel, single step method for the determination of seven ink photo-initiators in carton packed milk samples is described. Solid-phase microextraction (SPME) and gas chromatography (GC), combined with mass spectrometry (MS), were used as sample preparation and determination techniques, respectively. Parameters affecting the performance of the microextraction process were thoroughly evaluated using uni- and multivariate optimization strategies, based on the use of experimental factorial designs. The coating of the SPME fibre, together with the sampling mode and the temperature were the factors playing a major influence on the efficiency of the extraction. Under final conditions, 1.5 mL of milk and 8.5 mL of ultrapure water were poured in a glass vessel, which was closed and immersed in a water boiling bath. A poly(dimethylsiloxane)-divinylbenzene (PDMS-DVB) coated fibre was exposed directly to the diluted sample for 40 min. After that, the fibre was desorbed in the injector of the GC-MS system for 3 min. The optimized method provided limits of quantification (LOQs) between 0.2 and 1 μg L⁻¹ and a good linearity in the range between 1 and 250 μg L⁻¹. The inter-day precision remained below 15% for all compounds in spiked whole milk. The efficiency of the extraction changed for whole, semi-skimmed and skimmed milk; however, no differences were noticed among the relative recoveries achieved for milk samples, from different brands, with the same fat content.     

Harnessing the power of electrophoresis and chromatography: Offline coupling of reverse phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry for analysis of host cell proteins in monoclonal antibody producing CHO cell line

Host cell proteins (HCPs) are widely regarded as a critical quality attribute for a biotherapeutic product. Bottom up MS is the present gold standard for HCP analysis but suffers from incomplete protein identification due to complex nature of the HCP mixture and limited separation efficiency of the preceding LC-based systems. In this paper, we present for the first time an application involving use of LC-CE-MS/MS platform for analysis of HCPs. It has been demonstrated that the proposed platform has been able to successfully identify 397 HCPs from the supernatants of recombinant Chinese hamster ovary cells, twice and thrice the number of proteins identified by the state-of-the-art LC-MS/MS (189 HCPs) and CE-MS/MS (128 HCPs) analyses, respectively. Of these, 225 HCPs were unique to the LC-CE-MS/MS approach and were not identified by either LC-MS/MS or CE-MS/MS. It is observed that the LC-CE-MS/MS platform combines the benefits of LC-MS/MS and CE-MS/MS techniques and identifies peptides in a wider range of size, pI, and hydrophobicity. Additionally, LC-CE-MS/MS also identified more HCPs associated with cellular components, molecular functions, biological processes, peptidases, and secretory proteins. The proposed approach would thus be a useful addition in HCP analysis and secretome studies of mAb-producing Chinese hamster ovary cells.     

Characterization of the protein profile of donkey's milk whey fraction

Characterization of the protein profile of the whey fraction from a milk sample taken from an individual donkey belonging to the 'Ragusana' species of the East of Sicily is reported. Direct RP-HPLC/electrospray ionization (ESI)-MS analysis of the whey fraction allowed the detection of some unknown components, together with the identification of already known whey proteins. Matrix-assisted laser desorption/ionization (MALDI)-TOF/MS and RP-HPLC/ESI-MS/MS analysis of the enzymatic digests of the unknown components resulted the identification and characterization of (1) two beta-casein fragments; (2) the sequence of donkey's serum albumin; and (3) the oxidized methionine forms of lysozyme B and alpha-lactoalbumin. One of the two beta-casein fragments corresponds to the sequence Val(176)-Arg(189) of the horse's beta-casein. The second one corresponds the C-terminal sequence Tyr(199)-Val(226) of the horse's beta-casein, with four amino acid substitutions (Q --> R(203), L/I --> P(206), F --> L(210) and P --> A(219)). Both fragments, reasonably arising by endogenous proteases cleavage of the donkey's beta-casein, could be potential biologically active peptides. Direct mass spectrometric sequence characterization of the detected donkey's serum albumin reveals the presence of the amino acid substitution Val --> Ile at position 497 with respect to the cDNA deduced sequence. The oxidized forms of lysozyme B and alpha-lactoalbumin are selectively oxidized at methionine 79 and methionine 90, respectively.     

Determination of flunixin and ketoprofen in milk by liquid chromatography-tandem mass spectrometry

A relatively fast, simple and very selective liquid chromatography-tandem mass spectrometry (LC-MS-MS) method for the detection of flunixin, its 5-hydroxymetabolite and ketoprofen in raw milk has been developed and validated. After a simple extraction with acetonitrile and partial evaporation of the organic phase, the extract was filtered and directly injected into the LC-MS-MS system on a Symmetry C₁₈ column. The parent ions were selected for further fragmentation with argon. The method developed was partially validated according to Commission Decision 2002/657/EC [Commission Decision 2002/657/EC implementing Council Directive 96/23/EC concerning the performance of analytical methods and the interpretation of results]. The validation parameters were linearity, specificity, repeatability, recovery and decision limit (CCα). CCα varied from 0.5 μg kg⁻¹ for flunixin and 5-hydroxyflunixin to 1 μg kg⁻¹ for ketoprofen.Holstein-Friesian cows were given either Ketofen^® or Finadyne^® via an intravenous injection at the maximum dose as written in the instructions. Cows were milked twice a day and all samples were analysed by the method described. The highest concentrations found for ketoprofen, flunixin and 5-hydroxyflunixin were 2.5, 6.7 and 590 μg l⁻¹, respectively. The concentration of 5-hydroxyflunixin declined rapidly to concentrations below the MRL value of 40 μg l⁻¹. It can be concluded that the withdrawal time proposed by the pharmaceutical companies, 12 h after the last dosing, is acceptable for both compounds.     

Multi-component analysis (sterols, tocopherols and triterpenic dialcohols) of the unsaponifiable fraction of vegetable oils by liquid chromatography-atmospheric pressure chemical ionization-ion trap mass spectrometry

A simple and sensitive method for the analysis of sterols, tocopherols and triterpenic dialcohols from the unsaponifiable fraction from oil samples in a single analytical run using liquid chromatography coupled to mass spectrometry was developed. With this method, the compounds could be detected directly after dissolving the unsaponifiable fraction in acetonitrile without necessity of time-consuming sample pre-treatment or derivatization. Separation of the analytes was carried out at room temperature, by using a C18 column (5 μm i.d. 3.0 mm × 250 mm) with a linear gradient of acetonitrile/water (0.01% acetic acid) at a flow rate of 1.5 mL/min. The full scan mass spectra of the investigated compounds were measured by an ion trap mass spectrometer equipped with an APCI ion source. The optimized methodology was suitable for the identification of 23 compounds belonging to different families present in olive oil and other kinds of oils, as well as for the quantification of 15 analytes (vs. their commercial standards).     

Low-molecular weight protein profiling of genetically modified maize using fast liquid chromatography electrospray ionization and time-of-flight mass spectrometry

In this work, the use of liquid chromatography coupled to electrospray time-of-flight mass spectrometry (LC-TOFMS) has been evaluated for the profiling of relatively low-molecular weight protein species in both genetically modified (GM) and non-GM maize. The proposed approach consisted of a straightforward sample fractionation with different water and ethanol-based buffer solutions followed by separation and detection of the protein species using liquid chromatography with a small particle size (1.8 μm) C(18) column and electrospray-time-of-flight mass spectrometry detection in the positive ionization mode. The fractionation of maize reference material containing different content of transgenic material (from 0 to 5% GM) led to five different fractions (albumins, globulins, zeins, zein-like glutelins, and glutelins), all of them containing different protein species (from 2 to 52 different species in each fraction). Some relevant differences in the quantity and types of protein species were observed in the different fractions of the reference material (with different GM contents) tested, thus revealing the potential use of the proposed approach for fast protein profiling and to detect tentative GMO markers in maize.     

Imatinib (Gleevec, Glivec) tumour tissue analysis by measurement of sediment and by liquid chromatography tandem mass spectrometry

The analysis of the signal transduction inhibitor imatinib in patient tumour tissue using LC and MS/MS is described. The anticancer agent is eluted over RP-C18 within 2 mm together with its internal standard STI571-d8. Calibration curves were prepared in red blood cells (RBC). For quantitative isolation of the RBC, measurement of sediment was applied. There were no indications of signal suppression by substances originating in the biological matrix. The limit of determination in tumour tissue was in the range of those recorded for RBC and plasma. The assay is selective and sensitive, with its robustness favouring the experimental application in clinical oncology and its routine use in animal experiments. The LOD was 4.5 ng per gram in tumour tissue.     

Application of multiwalled carbon nanotubes as sorbents for the extraction of mycotoxins in water samples and infant milk formula prior to high performance liquid chromatography mass spectrometry analysis

In this work, a simple and environmental friendly methodology has been developed for the analysis of a group of six mycotoxins with estrogenic activity produced by Fusarium species (i.e. zearalanone, zearalenone, α‐zearalanol, β‐zearalanol, α‐zearalenol, and β‐zearalenol), using microdispersive SPE (μ‐dSPE) with multiwalled carbon nanotubes as sorbent. Separation, determination, and quantification were achieved by HPLC coupled to ion trap MS with an ESI interface. Parameters affecting the extraction efficiency of µ‐dSPE such as pH of the sample, amount of multiwalled carbon nanotubes, and type and volume of elution solvent, were studied and optimized. The methodology was validated for mineral, pond, and wastewater as well as for powdered infant milk using 17β‐estradiol‐2,4,16,16,17‐d₅ (17β‐E₂‐D₅) as internal standard, obtaining recoveries ranging from 85 to 120% for the three types of water samples and from 77 to 115% for powdered infant milk. RSD values were lower than 10%. The LOQs achieved were in the range 0.05–2.90 μg/L for water samples and 2.02–31.9 μg/L for powdered infant milk samples.     

Application of matrix solid phase dispersion to the determination of imidacloprid, carbaryl, aldicarb, and their main metabolites in honeybees by liquid chromatography-mass spectrometry detection

A method based on matrix solid phase dispersion (MSPD) using C18 as dispersant and dichloromethane-methanol as eluent and liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (LC-APCI-MS) has been developed for the simultaneous determination of imidacloprid, 6-chloronicotinic acid, carbaryl, aldicarb, aldicarb sulfoxide, and aldicarb sulfone in honeybees.The proposed method was compared with liquid-liquid extraction (LLE) combined with LC-APCI-MS analysis. Spiked blank samples were used as standards to counteract the matrix effect observed in the chromatographic determination. Recovery studies were performed at different fortification levels. Average recoveries by MSPD varied from 61% of 6-chloronicotinic acid to 99% of aldicarb sulfoxide and relative standard deviations were equal or lower than 14%. Limit of detections ranged from 0.004 mg kg⁻¹ for imidacloprid to 0.09 mg kg⁻¹ for 6-chloronicotinic acid. Results obtained by both methods were compared, MSPD showed higher recoveries and sensitivity than LLE for most pesticides, except for carbaryl. As MSPD is easier to perform, faster, consumes less sample and organic solvents than LLE, its application for pesticide analysis in honeybees is suggested.     

LC–ESI/MS Analysis of Levodopa and Methyldopa (IS) in Beagle Dog Pharmacokinetic Study after Oral Administration and Domperidone Given in Advance

A simple, sensitive and accurate method was developed for the quantification of levodopa and methyldopa (IS) in beagle dog plasma by LC–ESI/MS, chromatographic separation was carried out by a Diamonsil C18 column (150 mm × 4.6 mm i.d., 5 mm) with an ODS guard column maintained at 30 °C. The mobile phase was methanol (A) and 0.5% formic acid aqueous solution (B) system in the gradient elution profile, the retention time of levodopa and IS were 4.8 and 6.1 min, respectively, linear range for levodopa concentration was 0.08‐20.0 μg/mL in plasma samples with a correlation coefficient(r) of 0.9978, the limit of detection was 32 ng/mL. CV of intra‐day and inter‐day assays were all less than 15%, mean recoveries of levodopa were all more than 90% in 0.32, 1.6 and 16.0 μg/mL concentrations of levodopa (n = 3). The validated method was successfully applied to the determination of levodopa in plasma samples, pharmacokinetic of levodopa following a single oral dose of compound levodopa tablets and antiemetic drug – domperidone administrated to beagle dogs has been carried out, the main pharmacokinetic parameters of levodopa with domperidone were as follows: T_max (0.50 ± 0.18) h, C_max (39.72 ± 7.91) μg/mL, t_l/2 (0.65 ± 0.07) h, AUC_o‐t (49.01 ± 12.13) μg·h/mL , AUC_o‐∞ (49.10 ± 12.16) μg·h/mL, we also evaluated the effect of domperidone on pharmacokinetics of levodopa in beagle dog. We thought non‐oral sustained‐release formulations should be a very good choice instead of this common oral dosage forms on the market, the test results can provide a reference for clinical trials on drug therapy of Parkinson‘s disease.     

Determination of avoparcin in animal tissues and milk using LC‐ESI‐MS/MS and tandem‐SPE

A highly sensitive and selective method using LC‐ESI‐MS/MS and tandem‐SPE was developed to detect trace amounts of avoparcin (AV) antibiotics in animal tissues and milk. Data acquisition using MS/MS was achieved by applying multiple reaction monitoring of the product ions of [M + 3H]³⁺ and the major product ions of AV‐α and ‐β at m/z 637 → 86/113/130 and m/z 649 → 86/113/130 in ESI(+) mode. The calculated instrumental LODs were 3 ng/mL. The sample preparation was described that the extraction using 5% TFA and the tandem‐SPE with an ion‐exchange (SAX) and InertSep C18‐A cartridge clean‐up enable us to determine AV in samples. Ion suppression was decreased by concentration rates of each sample solution. These SPE concentration levels could be used to detect quantities of 5 ppb (milk), 10 ppb (beef), and 25 ppb (chicken muscle and liver). The matrix matching calibration graphs obtained for both AV‐α (r >0.996) and ‐β (r >0.998) from animal tissues and milk were linear over the calibration ranges. AV recovery from samples was higher than 73.3% and the RSD was less than 12.0% (n = 5).     

Simultaneous determination of aflatoxin B1, B2, G1, and G2 in corn powder,edible oil,peanut butter,and soy sauce by liquid chromatography with tandem mass spectrometry utilizing turbulent flow chromatography

A novel fully automated method based on dual column switching using turbulent flow chromatography followed by liquid chromatography with tandem mass spectrometry was developed for the determination of aflatoxin B₁, B₂, G₁, and G₂ in corn powder, edible oil, peanut butter, and soy sauce samples. After ultrasound‐assisted extraction, samples were directly injected to the chromatographic system and the analytes were concentrated into the clean‐up loading column. Through purge switching, the analytes were transferred to the analytical column for subsequent detection by mass spectrometry. Different types of TurboFlow^TM columns, transfer flow rate, transfer time were optimized. The limits of detection and quantification of this method ranged between 0.2–2.0 and 0.5–4.0 μg/kg for aflatoxins in different matrixes, respectively. Recoveries of aflatoxins were in range of 83–108.1% for all samples, matrix effects were in range of 34.1–104.7%. The developed method has been successfully applied in the analysis of aflatoxin B₁, B₂, G₁, and G₂ in real samples.     

Current role of LC-MS in therapeutic drug monitoring

The role of liquid chromatography coupled with mass spectrometry (LC-MS) techniques in routine therapeutic drug monitoring activity is becoming increasingly important. This paper reviews LC-MS methods published in the last few years for certain classes of drugs subject to therapeutic drug monitoring: immunosuppressants, antifungal drugs, antiretroviral drugs, antidepressants and antipsychotics. For each class of compounds, we focussed on the most interesting methods and evaluated the current role of LC-MS in therapeutic drug monitoring.     

Isolation and determination of paspalitrem-type tremorgenic mycotoxins using liquid chromatography with diode-array detection

A liquid chromatographic (LC) method is described for the isolation and determination of the tremorgenic mycotoxins paxilline (Penicillium paxilli NRRL 6110), paspaline, paspalinine and paspalicine (Claviceps paspali). Following a Soxhlet extraction of a mould-contaminated matrix using chloroform, the crude extract was partitioned between hexane and 80% aqueous methanol. The latter fraction, containing the desired toxin(s), was evaporated to dryness, the residue dissolved in methylene chloride and the solution analysed by liquid chromatography using a Supelcosil LC-Si column eluted with methylene chloride-diethyl ether (9 + 1, v/v). A mixture containing standards of these compounds was similarly analysed. All toxins were detected using a UV diode-array detector. The generated UV spectra and chromatographic data of the standard toxins were stored in a computer as a library and used to identify these toxins in a crude mixture. The purity of the separated peaks and the amount of toxin in the crude mixture were also determined. The toxins were isolated by selectively collecting the eluted peaks using a programmable fraction collector equipped with a peak level sensor. Further confirmation of compound identity was achieved by mass spectrometry using the direct inlet probe method. In comparison with methods used previously to isolate these toxins, the present technique is fast and allows the acquisition of complete UV spectral information and chromatographic data and the isolation of multiple toxins in a single chromatographic operation.