DNA microsatellite analysis using ion-pair reversed-phase high-performance liquid chromatography

Genotyping based on short tandem repeat (STR) regions is used in human identification and parentage testing, gene mapping studies, cancer diagnostics, and diagnosis of hereditary diseases. Analysis of STR systems using slab gel electrophoresis requires lengthy and labor-intensive procedures. Therefore, alternative methods such as capillary electrophoresis or ion-pair reversed-phase high-performance liquid chromatography (IPRP HPLC) have been used to analyze DNA. IPRP HPLC offers an attractive substitute to gel electrophoresis for STR analysis because of the reduced analysis time, and there is no need for the waste disposal associated with radioisotopic, enzyme-linked, or fluorescence detection systems. We evaluated the use of IPRP HPLC for the sizing and typing of STR alleles from the HUMTHO1 locus. The IPRP HPLC conditions (column temperature, flow rate, percent organic modifier per minute) were optimized for the separation of PCR products. Using the optimized separation conditions, the alleles of the HUMTHO1 system were sized in their native state (double standard) with the use of internal markers. The typing results correlated 100% to accepted methods of DNA typing. The analysis time for the HUMTHO1 locus was less than 14 min, and the alleles could be peak captured for further examination following such as sequencing.     

Overload for ionized solutes in reversed-phase high-performance liquid chromatography

Overloading occurs for submicrogram quantities of ionized solutes particularly when using low ionic strength mobile phases at low pH (e.g., formic acid), even with highly inert silica RP-HPLC columns of normal dimensions. Much higher loads can produce a sharp L-shaped peak with retention above the column void volume, in line with the hypothesis that a small number of high-energy sites fill first and are rapidly overloaded, followed by a much larger number of weaker sites. However, charged acids and bases show identical overloading behavior; overloading is reduced as the mobile-phase ionic strength is increased. These findings raise questions about the physical nature of the strong sites. The rapid overloading of silica and purely polymeric phases could be explained by mutual repulsion of ionic species or their inability to fully penetrate the hydrophobic structure of the phase. However, these alternative hypotheses cannot readily explain the high total saturation capacities obtained using frontal analysis. Ion pairing with trifluoroacetic acid may reduce overload, while the effect is less important for formate or phosphate buffers. A surface layer of acetonitrile is not a prerequisite for rapid overloading, as shown by studies using purely aqueous buffers.     

Determination of phospholipids from pulmonary surfactant using an on-line coupled silica/reversed-phase high-performance liquid chromatography system.

A basic normal-phase HPLC separation of phospholipids can be improved by introducing a limited contribution of solvophobic retention. For this purpose, the effect of an additional alkylsilica (C18) column of variable length coupled in series with a silica column was investigated. With increasing percentage of reversed phase in this system, the retention of phosphatidylglycerol increased. Phosphatidylinositol and phosphatidylserine were separated into molecular species. The "selective retention" defined in this study permits an evaluation of the solvophobic retention of phospholipids in the coupled system. An alternative column switching procedure is used for specific applications of the biphasic separation on chosen phospholipids. With this system, determination of phosphatidylglycerol and six other phospholipids from pulmonary surfactant could be performed.     

Electrospray ionization mass spectrometry coupled to reversed-phase ion-pair high-performance liquid chromatography for quantitation of sodium borocaptate and application to pharmacokinetic analysis

We have developed a quantitative assay using electrospray ionization mass spectrometry coupled to reversed-phase ion-pair liquid chromatography (LC/MS) for quantitation of sodium borocaptate (BSH) in human plasma. The assay was developed using a Micromass Q-TOF II mass spectrometer equipped with an orthogonal electrospray source. The mobile phase was a 1:1 solution of methanol and 5 mM aqueous tetrabutylammonium acetate flowing at 0.2 mL/min, and the chromatography was performed using a Machery-Nagel Nucleosil C18 column. Plasma samples from patients who had received an intravenous infusion of sodium borocaptate (Na2B12H11SH), frequently referred to as BSH, were prepared for analysis by precipitation with acetonitrile. Following this, the supernatants were collected, and 40 microL was injected onto the column for analysis. The LC/MS assay was linear over a BSH plasma concentration range of 20-0.5 microg/mL with acceptable variability for both intra- and interassay precision. The LC/MS assay was used to generate pilot pharmacokinetic data for the plasma disposition of BSH in humans. The disposition of BSH was found to be consistent with a two-compartment model with first-order elimination from the central compartment. The mean total body plasma clearance was 95.7 +/- 30.8 m/min and the harmonic mean terminal half-life was 3.6 h.     

Probing the binding behavior and conformational states of globular proteins in reversed-phase high-performance liquid chromatography.

Reversed-phase high-performance liquid chromatography (RP-HPLC) is a widely used technique for the separation of proteins under low pH aquo-organic solvent gradient elution conditions, typically carried out at ambient temperatures. These conditions can however induce conformational effects with proteins as evident from changes in their biological or immunological activities. By monitoring the influence of temperature on the retention and band-broadening characteristics of proteins, the role of conformational processes in these lipophilic environments can be examined. These processes can then be interpreted in terms of a two-state model involving a native (N) and a fully unfolded species (U) or more complex folding/unfolding models. In the present study, the gradient elution RP-HPLC behavior of sperm whale myoglobin (SWMYO) and hen egg white lysozyme (HEWL) has been investigated at temperatures between 5 and 85 degrees C with n-octadecyl (C18)- and n-butyl (C4)-silica reversed-phase sorbents. The interaction of these proteins with these reversed-phase sorbents has also been examined in terms of the contributions that the heme prosthetic group of SWMYO and the disulfide bonds in HEWL make to the stabilization of the native conformation of these proteins in these hydrophobic environments. The observed interconversions of multiple peak zones of SWMYO and HEWL in the presence of C18 and C4 ligands have been subsequently analyzed in terms of the unfolding processes that these proteins can undergo at low pH and at elevated temperatures. The ability of hydrocarbonaceous ligands to trap ensemblies of partially unfolded conformational intermediates of proteins in these perturbing environments has been examined. Pseudo-first-order rate constants have been derived for these processes from analysis of the dependencies on time of the concentration of the different protein species at specified temperatures. The relationship of these processes to the conformational transitions that these proteins can undergo via molten globule-like intermediates (i.e., compact denatured states with a significant amount of residual secondary structure) in solution has also been examined. This study thus further documents an experimental strategy to assess the folding/unfolding behavior of globular proteins in the presence of hydrophobic surfaces and aquo-organic solvents, whereby the system parameters can potentially affect the preservation of native conformations, and thus the function, of the protein under these conditions.     

Temperature-programmed high-performance liquid chromatography coupled to isotope ratio mass spectrometry

The utility of liquid chromatography coupled to the isotope ratio mass spectrometry technique (LC-IRMS) has already been established through a variety of successful applications. However, the analytical constraint related to the use of aqueous mobile phases limits the LC separation mechanism. We report here a new strategy for high-precision (13)C isotopic analyses based on temperature-programmed LC-IRMS using aqueous mobile phases. Under these conditions, the isotopic precision and accuracy were studied. On one hand, experiments were carried out with phenolic acids using isothermal LC conditions at high temperature (170 degrees C); on the other hand, several experiments were performed by ramping the temperature, as conventionally used in a gas chromatography-based method with hydrosoluble fatty acids and pulses of CO 2 reference gas. In isothermal conditions at 170 degrees C, despite the increase of the CO 2 background, p-coumaric acid and its glucuronide conjugate gave reliable isotopic ratios compared to flow injection analysis-isotopic ratio mass spectrometry (FIA-IRMS) analyses (isotopic precision and accuracy are lower than 0.3 per thousand). On the opposite, for its sulfate conjugate, the isotopic accuracy is affected by its coelution with p-coumaric acid. Not surprisingly, this study also demonstrates that at high temperature (170 degrees C), a compound eluting with long residence time (i.e., ferulic acid) is degraded, affecting thus the delta (13)C (drift of 3 per thousand) and the peak area (compared to FIA-IRMS analysis at room temperature). Quantitation is also reported in isothermal conditions for p-coumaric acid in the range of 10-400 ng/mL and with benzoic acid as an internal standard. For temperature gradient LC-IRMS, in the area of the LC gradient (set up at 20 degrees C/min), the drift of the background observed produces a nonlinearity of SD (delta (13)C) approximately 0.01 per thousand/mV. To circumvent this drift, which impacts severely the precision and accuracy, an alternative approach, i.e., eluting the compound on the plateau of temperature studied was reported here. Other experiments with temperature-programmed LC-IRMS experiments are also reported with the presence of methanol in the injected solution to mimic residual solvent originating from the sample preparation or to slightly increase the solubility of the targeted compound for high-precision measurement.     

Reversed-phase capillary liquid chromatography coupled on-line to capillary electrophoresis immunoassays

Capillary reversed-phase liquid chromatography (RPLC) was coupled on-line to competitive capillary electrophoresis immunoassay (CEIA) to improve concentration sensitivity of the competitive CEIA and to provide a means for detecting multiple species that cross-react with antibody. A competitive CEIA for glucagon was used for demonstration of this technique. Five-microliter samples were injected onto a 4-cm-long by 50-micron-i.d. RPLC column. Sample was desorbed by gradient elution, mixed on-line with fluorescently labeled glucagon and anti-glucagon, incubated in a continuous-flow reaction capillary, and analyzed by capillary electrophoresis with flow-gated injection and laser-induced fluorescence detection. Electrophoretic analysis of the reactor stream was performed every 1.5 s, allowing nearly continuous monitoring of the RPLC separation. Preconcentration achieved by RPLC allowed improvement in the detection limit from 760 to 20 pM. Addition of the RPLC column also allowed multiple cross-reactive species to be differentiated by first separating them chromatographically and then detecting them with the immunoassay. The technique was used to measure glucagon secretion from single islets of Langerhans and to differentiate cross-reactive forms of glucagon with one assay.     

Determination of aromatic and sulfur-containing amino acids, peptides, and proteins using high-performance liquid chromatography with photolytic electrochemical detection

Aromatic amino acids, sulfur-containing amino acids, peptides containing such constituents, and proteins can now be detected in high-performance liquid chromatography by the use of on-line, postcolumn, continuous photolytic derivatization with electrochemical (HPLC-hv-EC) detection. The overall approach is a very simple, reproducible, rapid, and fully automatable approach for the determination of certain amino acids, peptides, and proteins with excellent selectivity, sensitivity, and linearities of response. Dual-electrode response ratios, lamp-on/lamp-off behavior, and chromatographic capacity factors all contribute to the enhanced selectivity of the overall HPLC-hv-EC determination for these particular classes of bioorganics and biopolymers. The analytical figures of merit, chromatography detection, and method validation approaches have all been optimally derived and demonstrated reproducible. Applications of the basic methodology to real-world samples are demonstrated and validated.     

Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer

Online liquid chromatography-mass spectrometric (LC-MS) analysis of intact proteins (i.e., top-down proteomics) is a growing area of research in the mass spectrometry community. A major advantage of top-down MS characterization of proteins is that the information of the intact protein is retained over the vastly more common bottom-up approach that uses protease-generated peptides to search genomic databases for protein identification. Concurrent to the emergence of top-down MS characterization of proteins has been the development and implementation of the stable isotope labeling of amino acids in cell culture (SILAC) method for relative quantification of proteins by LC-MS. Herein we describe the qualitative and quantitative top-down characterization of proteins derived from SILAC-labeled Aspergillus flavus using nanoflow reversed-phase liquid chromatography directly coupled to a linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FTICR-MS). A. flavus is a toxic filamentous fungus that significantly impacts the agricultural economy and human health. SILAC labeling improved the confidence of protein identification, and we observed 1318 unique protein masses corresponding to 659 SILAC pairs, of which 22 were confidently identified. However, we have observed some limiting issues with regard to protein quantification using top-down MS/MS analyses of SILAC-labeled proteins. The role of SILAC labeling in the presence of competing endogenously produced amino acid residues and its impact on quantification of intact species are discussed in detail.     

Identification and quantification of 77 pesticides in groundwater using solid phase coupled to liquid-liquid microextraction and reversed-phase liquid chromatography

This paper describes a method for the extraction, separation, identification, and quantification of 77 pesticides (neutral, acidic, and basic) including some s-triazine metabolites. The method is appropriate for organically (e.g. with humic acids) highly loaded groundwater samples. A comparative study of a pH-controlled mixed solid phase (LiChroprep RP18/LiChrolut EN) extraction with different desorption solvents (acetonitrile or acetonitrile and dichloromethane/methanol) is elaborated. A subsequent liquid-liquid microextraction reduces matrix effects. The pesticides in the sample are separated using RP-HPLC, detected, and identified by diode array. The efficiency is illustrated on a natural groundwater sample from a phreatic aquifer.     

Automated instrumentation for comprehensive two-dimensional high-performance liquid chromatography of proteins

A comprehensive two-dimensional (2-D) liquid chromatographic separation system is presented. The system uses a microbore cation exchange column, operated under gradient conditions, as the first dimension separation. Effluent from this first column alternately fills one of two loops on a computer-controlled eight-port valve. A second pump then forces loop material onto a second column, a size exclusion column. UV detection is used, and the system is applied to the separation of protein standards and serum proteins. The 2-D system has a higher resolving power and peak capacity than either of the two columns used alone. The entire first column effluent is analyzed on the second column in virtually the same time it takes to complete the first column separation, without the use of stopped flow methods. The entire system is automated and operated under computer control. Three-dimensional (3-D) data representation provides a means of viewing peak profiles in either separation dimension and contour mapping of the 3-D data provides a more reliable means of peak identification from run to run than that provided by single-column elution times.     

A multidimensional differential proteomic platform using dual-phase ion-exchange chromatography-polyacrylamide gel electrophoresis/reversed-phase liquid chromatography tandem mass spectrometry

Differential proteomic analysis has arisen as a large-scale means to discern proteome-wide changes upon treatment, injury, or disease. Tandem protein separation methods are required for large-scale differential proteomic analysis. Here, a novel multidimensional platform for resolving and differentially analyzing complex biological samples is presented. The platform, collectively termed CAX-PAGE/RPLC-MSMS, combines biphasic ion-exchange chromatography with polyacrylamide gel electrophoresis for protein separation, quantification, and differential band targeting, followed by capillary reversed-phase liquid chromatography and data-dependent tandem mass spectrometry for quantitative and qualitative peptide analysis. CAX-PAGE provides high protein resolving power with a theoretical peak capacity of 3570, extendable to 7600, a wide protein mass range verified from 16 to 273 kDa, and reproducible differential sample comparison without the added expense of fluorescent dyes and imaging equipment. Demonstrated using a neuroproteomic model, CAX-PAGE revealed an increased number of differential proteins, 137, compared with 82 found by 2D difference gel electrophoresis. When combined with RPLC-MSMS for protein identification, an additional quantification step is performed for internal validation, confirming a 2-fold or greater change in 89% of identified differential targets.     

Wavelet-based method for noise characterization and rejection in high-performance liquid chromatography coupled to mass spectrometry

We present a new method for rejecting noise from HPLC-MS data sets. The algorithm reveals peptides at low concentrations by minimizing both the chemical and the random noise. The goal is reached through a systematic approach to characterize and remove the background. The data are represented as two-dimensional maps, in order to optimally exploit the complementary dimensions of separation of the peptides offered by the LC-MS technique. The virtual chromatograms, reconstructed from the spectrographic data, have proved to be more suitable to characterize the noise than the raw mass spectra. By means of wavelet analysis, it was possible to access both the chemical and the random noise, at different scales of the decomposition. The novel approach has proved to efficiently distinguish signal from noise and to selectively reject the background while preserving low-abundance peptides.     

Silica xerogel as a continuous column support for high-performance liquid chromatography

A preliminary study of the chromatographic performance and permeability of a continuous silica xerogel column under reversed-phase HPLC conditions was performed. A porous chromatographic support was synthesized inside a 0.32 mm i.d. × 13 cm fused silica tube from potassium silicate solution and derivatized with dimethyloctadecylchlorosilane. The plate height at 0.01 cm/s (0.5 μL/min), near the apparent optimum linear velocity, was about 65 μm. The column efficiencies in terms of numbers of plates per meter were 5000 and 13?000 for ethyl benzoate (k = 0.8) and naphthalene (k = 2.0), respectively, at 0.5 μL/min. The major parameter affecting column efficiency was the heterogeneous morphology of the xerogel, modifications to which are expected to improve chromatographic performance. The column provided efficiencies comparable to those reported for continuous polymeric columns but less than that previously reported for a continuous silica column. Gradient elution mode was demonstrated with a mixture of polycyclic aromatic hydrocarbons. The column was highly permeable, exhibiting a linear dependence of pressure to flow rate and a back pressure of only 632 psi at 10 μL/min when a 95% aqueous mobile phase was used.     

Separation of nonionic surfactants by capillary electrophoresis and high-performance liquid chromatography

Fatty alcohol ethoxylates (FAEs) are applied in commercial formulations (laundry detergents) as complex mixtures of alkyl and ethoxylate homologues. Therefore, efficient analytical methods are required for product control. Capillary electrophoresis, a modern analytical separation technique, was used to separate FAEs in technical products and household formulations after derivatization with phthalic anhydride. The well-established high-performance liquid chromatography was used as reference and supplementary method. UV detection after derivatization with phenyl isocyanate or light scattering detection has been carried out. Sample components have been identified by standard addition or by comparison to known products. The peak pattern can be considered as a "fingerprint" of the product and is characteristic for a defined composition.     

A reversed-phase high-performance liquid chromatographic method for the determination of soya bean proteins in bovine milks

A reversed-phase high-performance liquid chromatographic method was designed for the quantitation of soya bean proteins in bovine milks. The method consisted of a linear binary gradient, acetonitrile-water-0.1% trifluoroacetic acid, at a flow rate of 1 mL/min and a temperature of 50 degrees C which resulted in a separation time for soya bean proteins of 11 min. Calibration by the external standard method using a soya bean protein isolate as standard was employed, and the method was validated by evaluating precision, accuracy, and robustness. This method was shown to be useful for the analysis of soya bean proteins in bovine milks spiked with soya bean protein isolate; soya bean protein concentrations of approximately 13 microg/g of bovine milk could be detected by using the optimized method. The results obtained for some of the bovine milks were compared with those obtained by the method of standard additions.     

Monolithic porous polymer layer for the separation of peptides and proteins using thin-layer chromatography coupled with MALDI-TOF-MS

Plates for thin-layer chromatography (TLC) with an attached layer of porous polymer monolith have been prepared and used for the separation of small molecules, peptides, and proteins. The 50-200-mum. thin poly(butyl methacrylate-co-ethylene dimethacrylate) layers were prepared in situ using UV-initiated polymerization. Precise control of the reaction conditions enables the preparation of monolithic layers with a well-defined porous structure that determines the chromatographic performance. Compared to conventional TLC and high-performance TLC using precoated layers based on silica, the small layer thickness and absence of any binder is expected to improve both retention characteristics and separation efficiency of the polymer-based monolithic thin-layer chromatographic plates. Spots of the separated compounds were first detected using typical UV imaging. Since the monolithic thin layers can be also prepared directly on the stainless steel MALDI carrier plate, the separation in TLC format can be coupled with MALDI-TOF-MS. Application of a conventional MALDI matrix facilitated desorption and ionization of peptides and proteins for molecular weight determination of the separated compounds.     

Capillary array high-performance liquid chromatography of nucleic acids and proteins

An array of monolithic poly(styrene/divinylbenzene) capillaries with individual column thermostats was constructed to demonstrate its utility for the separation of nucleic acids, proteins, and tryptic digests in combination with UV absorbance detection. Because of polymerization-related variation in surface area of monolithic columns, the concentration of acetonitrile required for elution of DNA fragments in denaturing HPLC may vary sufficiently to affect the degree of denaturation. Modulation of column temperature offers a convenient way to harmonize elution profiles among columns. Individual regulation of column temperature also provides the means to determine rapidly in a single parallel run the optimum temperature for resolution of biomolecules. Given the high reproducibility of separations among columns and the ease with which poly(styrene/divinylbenzene)-based stationary phases can be modified to accommodate different modes of chromatography, such arrays will find broad applicability in proteogenomics.