Off-line Coupling Research Articles

Shotgun Identification of the Structural Proteome of Shrimp White Spot Syndrome Virus and iTRAQ Differentiation of Envelope and Nucleocapsid Subproteomes

White spot syndrome virus (WSSV) is a major pathogen that causes severe mortality and economic losses to shrimp cultivation worldwide. The genome of WSSV contains a 305-kb double-stranded circular DNA, which encodes 181 predicted ORFs. Previous gel-based proteomics studies on WSSV have identified 38 structural proteins. In this study, we applied shotgun proteomics using off-line coupling of an LC system with MALDI-TOF/TOF MS/MS as a complementary and comprehensive approach to investigate the WSSV proteome. This approach led to the identification of 45 viral proteins; 13 of them are reported for the first time. Seven viral proteins were found to have acetylated N termini. RT-PCR confirmed the mRNA expression of these 13 newly identified viral proteins. Furthermore iTRAQ (isobaric tags for relative and absolute quantification), a quantitative proteomics strategy, was used to distinguish envelope proteins and nucleocapsid proteins of WSSV. Based on iTRAQ ratios, we successfully identified 23 envelope proteins and six nucleocapsid proteins. Our results validated 15 structural proteins with previously known localization in the virion. Furthermore the localization of an additional 12 envelope proteins and two nucleocapsid proteins was determined. We demonstrated that iTRAQ is an effective approach for high throughput viral protein localization determination. Altogether WSSV is assembled by at least 58 structural proteins, including 13 proteins newly identified by shotgun proteomics and one identified by iTRAQ. The localization of 42 structural proteins was determined; 33 are envelope proteins, and nine are nucleocapsid proteins. A comprehensive identification of WSSV structural proteins and their localization should facilitate the studies of its assembly and mechanism of infection.

Off-line coupling of preparative capillary zone electrophoresis with microwave-assisted acid hydrolysis and matrix-assisted laser desorption ionization mass spectrometry for protein sequencing

An off-line coupling of capillary electrophoresis (CE) with microwave-assisted acid hydrolysis/matrix-assisted laser desorption ionization mass spectrometry (MAAH/MALDI) has been developed for protein identification and characterization. Preparative scale protein separations enable collection of 10–50 pmol of purified cytochrome c for subsequent sequencing using MAAH/MALDI. To reduce protein adsorption onto the silica surface, the cationic surfactant-based coatings, dimethylditetradecylammonium bromide and dimethyldioctadecylammonium bromide, are employed. The choice of the buffer conditions is critical for both the preparative CE and MAAH/MALDI method. The use of high buffer concentrations (100 mM Bis–tris) reduces electromigration dispersion, but suppressed MALDI ionization such that a peptide sequence coverage of only 80% was achieved at a sample loading of 40 g L −1 of each cytochrome c. By reducing the buffer concentration to 25 mM Bis–tris, the sequence coverage increased to 95% at a sample loading of 40 g L −1.

Synthesis and structural study of copolymers of l-lactic acid and bis(2-hydroxyethyl terephthalate)

Poly(ethylene terephthalate)–poly(lactic acid) (PET–PLLA) copolyesters were synthesized by the melt reaction of bis(2-hydroxyethyl terephthalate) (BHET) with l-lactic acid oligomers (OLLA) in the presence of SnCl 2, H 2O– p-toluene sulfonic acid, H 2O catalytic system. The 1H and 13C NMR studies confirm the incorporation of lactate units in PET chains after reaction. Copolyesters containing nearly equimolar terephthalate/lactate ratio are not completely random and present some block-copolymer character, while the microstructure of PET-rich copolyesters is a random one. Due to a longer PET sequence length, the latter exhibit a melting point close to 210 °C while the other ones are amorphous. SEC/MALDI-TOF MS off-line coupling was used to obtain the absolute average molar masses of the copolyesters. The results indicate that the conventional polystyrene calibration method leads to a strong overestimation of PET–PLLA molar masses, while the M n ¯ determined by NMR is much closer to the SEC/MALDI value.

Structure elucidation of arabinoxylan isomers by normal phase HPLC–MALDI-TOF/TOF-MS/MS

Normal phase-high performance liquid chromatography (NP-HPLC) coupled to matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight (MALDI-TOF/TOF) tandem mass spectrometry is evaluated for the detailed structural characterization of various isomers of arabinoxylan (AX) oligosaccharides produced from endo-β-(1→4)-xylanase (endoxylanase) digestion of wheat AX. The fragmentation characteristics of these oligosaccharides upon MALDI-TOF/TOF high-energy collision induced dissociation (CID) were investigated using purified AX oligosaccharide standards labeled at the reducing end with 2-aminobenzoic acid (2-AA). A variety of cross-ring cleavages and ‘elimination’ ions in the fragment ion spectra provided extensive structural information, including Ara f substitution patterns along the xylan backbone and comprehensive linkage assignment. The off-line coupling of this MALDI-CID technique to capillary normal phase HPLC enabled the separation and identification of isomeric oligosaccharides (DP 4–8) produced by endoxylanase digestion of AX. Furthermore, this technique was used to characterize structurally different isomeric AX oligosaccharides produced by endoxylanase enzymes with different substrate specificities.

Off-line coupling of pressurized liquid extraction and LC/ED for the determination of retinyl acetate and tocopherols in infant formulas

An analytical methodology including pressurized liquid extraction (PLE) as sample treatment to isolate retinyl acetate and tocopherols from infant formulas has been developed. The milk extracts were kept at −18 °C for 30 min and after filtration could be injected directly into the chromatographic system. Thus, a rapid and simple routine control method of these products is possible. The parameters affecting both the extraction process and the liquid chromatography (LC) system were optimized. PLE was performed using one cycle of extraction during a static time of 5 min. Methanol was chosen as the extraction solvent for a temperature of 50 °C. Chromatographic separation was accomplished using a RP-18 column; the mobile phase used was methanol–water (94:6, v/v) containing 2.5 mM acetic acid/sodium acetate buffer. Electrochemical detection in amperometric mode with a glassy carbon electrode at +1100 mV was applied. The proposed methodology was successfully used for the determination of retinyl acetate, δ-tocopherol, (β + γ)-tocopherol and α-tocopherol in different infant formulas. The analytes were evaluated in the same chemical form present in the samples. Recoveries were between 92 and 106%. A certified reference material of milk powder was also analyzed.

Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry with size‐exclusion chromatographic fractionation for structural characterization of synthetic aliphatic copolyesters

We report matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and off-line coupling of size-exclusion chromatography with MALDI-TOFMS analysis (SEC/MALDI-TOFMS) methods for the detailed characterization of poly[(R,S)-3-hydroxybutyrate-co-L-lactic acid], P[(R,S)-3HB-co-LA], and poly[(R,S)-3-hydroxybutyrate-co-epsilon-caprolactone], P[(R,S)-3HB-co-CL], copolymer samples which are expected to be used in special medical application as scaffolds for cartilage and soft tissue engineering. The novel copolyesters contained randomly distributed (R,S)-3-hydroxybutyrate structural units, were synthesized by transesterification of the corresponding homopolymers, i.e. atactic poly[(R,S)-3-hydroxybutyrate], a-PHB, and poly(L-Lactide) (PLLA) or poly(epsilon-caprolactone) (PCL), respectively. The MS methods used for the characterization of the resulting polydisperse copolyester samples were supported by classical methods (NMR, SEC). The structures of individual copolyester macromolecules, including end-group chemical structures, were established using initially MALDI-TOFMS and then SEC/MALDI-TOFMS. The compositions of the copolyesters were determined by two methods, namely based on 1H NMR and MALDI-TOF spectra. The two sets of values showed good agreement. The sequence distribution was determined using the signal intensities of individual copolyester macromolecules, which appeared in MALDI-TOF mass spectra. Furthermore, sequence analysis gave information about the degree of transesterification. The copolyesters synthesized, with only one exception, were demonstrated to be almost random, which implies that the ester-ester exchange was close to completion.

Alteration of Steroid Hormone Balance in Juvenile Turbot (Psetta maxima) Exposed to Nonylphenol, Bisphenol A, Tetrabromodiphenyl Ether 47, Diallylphthalate, Oil, and Oil Spiked with Alkylphenols

In recent years, concern has been raised about the ability of some classes of environmental contaminants to disrupt the endocrine system of both humans and wildlife. In this study, juvenile turbots (Psetta maxima) were exposed under laboratory conditions to selected waterborne contaminants: oil, oil spiked with alkylphenols, bisphenol A, diallylphthalate, tetrabrominated diphenyl ether 47, and p-nonylphenol as a positive control for "estrogenic-type" effects. This work focused on sex steroids, because these hormones play a key role in the reproduction process. Analytical procedures, involving the off-line coupling of solid phase extraction and gas chromatography/mass spectrometry, were developed for the determination of 12 endogenous sex steroids levels in fish plasma, bile, and gonads. Because of the sexual immaturity of the fish used in this study, however, only six steroids could be detected in juvenile turbots. Bisphenol A and p-nonylphenol exhibited the highest potency towards steroids dynamics, lowering the ratio of androgens to estrogens in all three studied matrices. However, these two chemicals had different modes of action, because p-nonylphenol induced a decrease of androstenedione and 11-ketotestosterone levels, whereas bisphenol A exposure led to an elevation of estrone level. Overall, these two chemicals seemingly disrupted the activity of some steroidogenesis enzymes, leading to serious hormonal imbalance in juvenile turbot.

Comparative Study of [Three] LC−MALDI Workflows for the Analysis of Complex Proteomic Samples

Large-scale proteomic analyses frequently rely on high-resolution peptide separation of digested protein mixtures in multiple dimensions to achieve accuracy in sample detection and sensitivity in dynamic range of coverage. This study was undertaken to demonstrate the feasibility of MALDI MS/MS with off-line coupling to HPLC for the analysis of whole cell lysates of wild-type yeast by three different workflows: SCX-RPHPLC-MS/MS, high-pH SAX-RPHPLC-MS/MS and RP (protein)-SCX-RPHPLC-MS/MS. The purpose of these experiments was to demonstrate the effect of a workflow on the end results in terms of the number of proteins detected, the average peptide coverage of proteins, and the number of redundant peptide sequencing attempts. Using 60 microg of yeast lysate, minor differences were seen in the number of proteins detected by each method (800-1200). The most significant differences were observed in redundancy of MS/MS acquisitions.

Analysis of human blood serum using the off-line coupling of capillary isoelectric focusing to matrix-assisted laser desorption/ionization time of flight mass spectrometry

Off-line coupling of capillary IEF (CIEF) with matrix-assisted laser desorption/ionization mass spectrometry was utilized for the analysis of human blood serum. Serum proteins were initially separated by CIEF, and fractions of the isoelectric separation were eluted sequentially to a MALDI-TOF MS sample target. During pressure elution of the CIEF sample, voltage was maintained across the capillary system utilizing a sheath flow arrangement to minimize band broadening induced by the laminar flow field. Both pI and mass information were obtained from the complex biological sample, similar to traditional 2-DE techniques, and the platform was faster (hours versus days), more automatable, and simpler than 2-DE. The volume of raw sample present in the actual analysis was approximately 100 nL, making this technique well suited for very rare specimens. Additionally, the speed and simplicity of the technology make it an attractive technique for performing initial comparative analyses of complex samples.

Electrospray interfacing of polymer microfluidics to MALDI-MS

The off-line coupling of polymer microfluidics to MALDI-MS is presented using electrospray deposition. Using polycarbonate microfluidic chips with integrated hydrophobic membrane electrospray tips, peptides and proteins are deposited onto a stainless steel target followed by MALDI-MS analysis. Microchip electrospray deposition is found to yield excellent spatial control and homogeneity of deposited peptide spots, and significantly improved MALDI-MS spectral reproducibility compared to traditional target preparation methods. A detection limit of 3.5 fmol is demonstrated for angiotensin. Furthermore, multiple electrospray tips on a single chip provide the ability to simultaneously elute parallel sample streams onto a MALDI target for high-throughput multiplexed analysis. Using a three-element electrospray tip array with 150 microm spacing, the simultaneous deposition of bradykinin, fibrinopeptide, and angiotensin is achieved with no cross talk between deposited samples. In addition, in-line proteolytic digestion of intact proteins is successfully achieved during the electrospray process by binding trypsin within the electrospray membrane, eliminating the need for on-probe digestion prior to MALDI-MS. The technology offers promise for a range of microfluidic platforms designed for high-throughput multiplexed proteomic analyses in which simultaneous on-chip separations require an effective interface to MS.

Molecular weights of poly(butyl cyanoacrylate) nanoparticles determined by mass spectrometry and size exclusion chromatography

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and size exclusion chromatography (SEC) were employed to elucidate the chemical composition, mean number average molecular weight ( M n), mean weight average molecular weight ( M w), and polydispersity (PD) of poly(butyl cyanoacrylate) (PBCA) manufactured by emulsion polymerisation. Both methods gave similar results for M n, but substantial differences were observed for M w and PD, with MALDI producing consistently lower values which could not be improved by off-line coupling of SEC and MALDI. MALDI gave a more detailed view on the chemical composition of the cyanoacrylate and revealed the presence of two additional polymer series with different end groups besides the expected PBCA series, which showed different retention in SEC. Their formation is explained by the secession/addition of formaldehyde from/to the regular polymer via (reverse) Knoevenagel reaction. In additional experiments, the influence of different pH on PBCA-NP during polymerisation was examined by comparison of polymerisation yield and particle diameter to their chemical composition as revealed by the MALDI spectra. The most uniform nanoparticles, with the highest polymerisation yield, narrowest particle size, and mass distribution were produced at pH 1.

Stereoselective determination of the major ibuprofen metabolites in human urine by off-line coupling solid-phase microextraction and high-performance liquid chromatography

A simple, rapid and sensitive off-line solid-phase microextraction method coupled to high-performance liquid chromatography was developed for the stereoselective analysis of the major ibuprofen metabolites in human urine samples. For this purpose, a carbowax/templated/resin coated fiber was used. Several parameters influencing the efficiency of the analyte extraction were explored. The chromatographic separation was achieved on a Chiralpak AS column using hexane:isopropanol (95:5 v/v) plus 0.05% trifluoroacetic acid as the mobile phase, at a flow-rate of 1.2 mL/min. Detection was carried out at 230 nm. The mean recoveries were between 1.4 and 1.6%, with R.S.D. values lower than 9.5 for both 2-OHIbu enantiomers, and between 3.7 and 5.7%, with R.S.D. values lower than 13.4 for all four COOHIbu stereoisomers. The method was linear over the 5–50 μg/mL concentration range and the quantification limit was 5 μg/mL for all metabolite stereoisomers. Within-day and between-day assay precision and accuracy for both metabolites were studied at three concentration levels of each stereoisomer (15, 30 and 45 μg/mL) and were lower than 15%.

Nanoflow liquid chromatography coupled to matrix-assisted laser desorption/ionization mass spectrometry: Sample preparation, data analysis, and application to the analysis of complex peptide mixtures

We report the development of a robust interface for off-line coupling of nano liquid chromatography (LC) to matrix-assisted laser desorption/ionisation-mass spectrometry (MALDI-MS) and its application to the analysis of proteolytic digests of proteins, both isolated and in mixtures. The interface makes use of prestructured MALDI sample supports to concentrate the effluent to a small sample plate area and localize the MALDI sample to a predefined array, thereby enriching the analyte molecules and facilitating automated MALDI-MS analysis. Parameters that influence the preparation of MALDI samples from the LC effluent were evaluated with regard to detection sensitivity, spectra quality, and reproducibility of the method. A procedure for data processing is described. The presented nano LC MALDI-MS system allowed the detection of several peptides from a tryptic digest of bovine serum albumin, at analyzed amounts corresponding to one femtomole of the digested protein. For the identification of native proteins isolated from mouse brain by two-dimensional gel electrophoresis, nano LC MALDI-MS increased the number of detected peptides, thereby allowing identification of proteins that could not be identified by direct MALDI-MS analysis. The ability to identify proteins in complex mixtures was evaluated for the analysis of Escherichia coli 50S ribosomal subunit. Out of the 33 expected proteins, 30 were identified by MALDI tandem time of flight fragment ion fingerprinting.

Dried-droplet laser ablation ICP-MS of HPLC fractions for the determination of selenomethionine in yeast

Offline coupling of high performance liquid chromatography (HPLC) to dried droplet laser ablation (LA) ICP-MS detection is described. The method is based on the offline spotting of HPLC fractions onto a substrate followed by LA introduction of the dried sample residues to an ICP-MS for elemental analysis. Quantitation of selenomethionine (SeMet) in yeast using species specific isotope dilution (ID) was achieved following digestion of samples in 4 M methanesulfonic acid and HPLC separation of species. Chromatographic fractions having retention times of 180–210 seconds were collected for each sample. Dried micro-droplets from each fraction were ablated from a polystyrene substrate and quantitated for SeMet. Concentrations of 3301 ± 18 and 3309 ± 24 μg g−1 (one standard deviation, n = 4) with RSDs of 0.55% and 0.73% were obtained based on measured 78Se/74Se and 82Se/74Se ratios, in good agreement with the values of 3309 ± 19 and 3305 ± 26 μg g−1 (one standard deviation, n = 4, RSDs of 0.58% and 0.79%), respectively, obtained by direct HPLC-ICP-MS analysis. The proposed method provides a satisfactory alternative technique for the quantitation of SeMet in yeast.

Optimization of a solid-phase microextraction procedure for the determination of herbicides by micellar electrokinetic chromatography.

The use of a different optimization procedure that involves Experimental Design (ED) and Artificial Neural Networks (ANN) for the off-line coupling solid-phase microextraction-micellar electokinetic chomatography (SPME-MEKC) is presented. This combination of ED and ANN, mathematical tools not previously used in SPME-MEKC optimization, allowed us to obtain good extraction efficiencies in the SPME procedure for the determination of a group of eleven triazine herbicides in groundwater samples. Both extraction and desorption steps were carried out by solution stirring at 900 rpm. Optimal conditions for the off-line SPME procedure were: extraction with a poly(dimethylsiloxane)/divinylbenzene SPME fiber for 120 min, 10% (w/v) NaCl, desorption time 40 min, and 70% (v/v) of methanol/buffer as desorption mixture. Detection limits lay between 0.80 microg L(-1) and 4.89 microg L(-1). Finally, the optimized method was applied to the determination of these compounds in spiked and non-spiked groundwater samples using a previously optimized MEKC separation.

Off-line coupling of non-aqueous reversed-phase and silver ion high-performance liquid chromatography–mass spectrometry for the characterization of rice oil triacylglycerol positional isomers

The determination of the triacylglycerol (TAG) profile in real world matrices is rather difficult as these compounds present a complex composition and are characterized by similar physico-chemical properties. This investigation is based on the high-performance liquid chromatography (HPLC) multidimensional determination of the TAG profile in terms of TAG species and positional isomers in a rice oil sample. The off-line bi-dimensional system was attained through the coupling of non-aqueous reversed-phase HPLC and silver ion (Ag)-HPLC. The primary column eluate was fractionated and the fractions of interest were then injected onto the secondary column, allowing the separation of several TAG positional isomers, unresolved in the first dimension. Peak assignment was carried out by combining retention data with atmospheric pressure chemical ionisation (APCI) MS spectra information. The fatty acid distribution along the glycerol backbone, determined by Ag-HPLC, was confirmed through diglyceride ion ratios derived from APCI-MS analysis. Method validation, where both precision and accuracy were measured, was carried out in preliminary applications on standard compounds. The analytical results obtained show that rice oil TAGs follow a distribution which can be considered typical for vegetable oils.

Application of off-line size-exclusion chromatographic fractionation–matrix assisted laser desorption ionization time of flight mass spectrometry for proanthocyanidin characterization

In this work, we wanted to devise a reliable method to characterize polymerized forms of tannins, their structural information and mass distribution. Size-exclusion chromatography (SEC) is a chromatographic technique used to determine molecular mass (weight) distributions of polymers. One important step in the data treatment is the modeling of the calibration curves. Polystyrenes (PS) are standards usually used because no commercial procyanidin (PC) standards are available. An off-line coupling of SEC and MALDI was carried out to measure differences between polystyrenes and procyanidins. Thus, a new calibration curve was established; from 1000 to 8000 Da, there is a good correlation between the MALDI and PS calibration curves, in this field the PS calibration is correct and enables true mass determination. For masses above 8000 Da, PS calibration overestimates the real molecular weight of PC, overestimation of 53%. And for masses below 1000 Da, PS calibration underestimates their real molecular weight (10–15%). This means that to truly characterize PC, calibration based on PC standards is required.

Result-driven strategies for protein identification and quantitation--a way to optimize experimental design and derive reliable results.

Uni- or multidimensional microcapillary liquid chromatography (microLC) matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) approaches have gained significant attention for quantifying and identifying proteins in complex biological samples. The off-line coupling of microLC with MS quantitation and MS/MS identification methods makes new result-dependent workflows possible. A relational database is used to store the results from multiple high performance liquid chromatography runs, including information about MALDI plate positions, and both peptide and protein quantitations, and identifications. Unlike electrospray methodology, where all the decisions about which peptide to fragment, must be made during peptide fractionations, in the MALDI experiments the samples are effectively "frozen in time". Therefore, additional MS and MS/MS spectra can be acquired, to promote more accurate quantitation or additional identifications until reliable results are derived that meet experimental design criteria. In the case of what can be designated the expression-dependent workflow, quantitation can be detached from identification and only peak pairs with biological relevant expression changes can be selected for further MS/MS analyses. Alternatively, additional MS/MS data can be acquired to confirm tentative peptide mass fingerprint hits in what is designated a search result-dependent workflow. In the MS data-dependent workflow, the goal is to collect as many meaningful spectra as possible by judiciously adjusting the acquisition parameters based on characteristics of the parent masses. This level of sophistication requires the development of innovative algorithms for these three result-dependent workflows that make MS and MS/MS analysis more efficient and also add confidence to experimental results.

Element and molecular mass spectrometry—an emerging analytical dream team in the life sciences

The recent literature on the combined applications of element (ICP, inductively coupled plasma) mass spectrometry and molecular (ESI, electrospray ionisation and MALDI, matrix assisted laser desorption ionisation) mass spectrometry in the life sciences is reviewed. Emphasis is put on investigations where both techniques have been used in a synergistic way with the aim of an analytical result with molecular specificity. Multi-element specificity and quantification are the key features of element MS, whereas molecular weight determination and structural information are those contributed by ESI and MALDI MS. The analytical applications cover the study of selenoproteins, phosphoproteins, metalloproteins, unmodified proteins, metallothioneins, phytochelatins, nucleic acids, arsenosugars, thyroid hormones, cobalamines, drugs and drug metabolites. Supported by on-line or off-line coupling to chromatographic or electrophoretic separation methods, the combined application of element and molecular mass spectrometry in all these studies has created the basis for new structural and/or quantitative insights, demonstrating the analytical excellence of this approach.

Off-line Coupling of Isotachophoresis and High Performance Liquid Chromatography for Determination of Flavonoids in Plant Extract

The use of isotachophoretic sample pretreatment coupled with high performance liquid chromatography for the analysis of some flavonoids occurring in plant extracts of Hypericum perforatum and Crataegus sp. is described. The samples were extracted with methanol by means of sonication in low temperature. The optimal leading electrolyte was used 10 mM Cl− as a leading ion in a buffer system at apparent pH*=7.2 (adjusted by TRIS) and terminating electrolyte was 50 mM boric acid at apparent pH*=8.2 (adjusted by barium hydroxide). The ITP electrolytes contained 20% (v/v) of methanol. To improve the sample pre-treatment, a pair of discrete ITP spacers defining the trapped constituents was used. Major components presented in the extracts were separated on a Discovery C18 and Discovery RP Amid C16 columns with a gradient mobile phase consisting of methanol, acetonitrile and diluted ortho-phosphoric acid. The quantification was performed by using external standards. The recoveries of the coupled ITP-HPLC analytical procedure were in the range of 91.2–95.6%.