Microbore HPLC/mass spectrometry for the analysis of peptide mixtures using a continuous flow interface

Microbore HPLC techniques have been combined with fast atom bombardment mass spectrometry to provide HPLC/MS capabilities for the analysis of mixtures of peptides and small proteins. The interface between the liquid chromatograph and mass spectrometer is a continuous flow direct insertion probe which contains a fused silica capillary that delivers the eluting solvent to the FAB source of the mass spectrometer at a rate of 5-10 microL/min. Data are presented for the analysis of several mixtures of peptides ranging in molecular weights from about 900 to 6000 daltons. In addition, the analysis of 100 pmol of a tryptic digest of whale myoglobin is shown where 16 of the possible 19 peptides were identified in the mass range m/z 2200-250. The advantages of this approach to HPLC/MS are a relatively high sensitivity because of the low flow rates and low background, and the ability to detect high molecular weight compounds.     

Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays

MOTIVATION: The most commonly utilized microarrays for mRNA profiling (Affymetrix) include 'probe sets' of a series of perfect match and mismatch probes (typically 22 oligonucleotides per probe set). There are an increasing number of reported 'probe set algorithms' that differ in their interpretation of a probe set to derive a single normalized 'signal' representative of expression of each mRNA. These algorithms are known to differ in accuracy and sensitivity, and optimization has been done using a small set of standardized control microarray data. We hypothesized that different mRNA profiling projects have varying sources and degrees of confounding noise, and that these should alter the choice of a specific probe set algorithm. Also, we hypothesized that use of the Microarray Suite (MAS) 5.0 probe set detection p-value as a weighting function would improve the performance of all probe set algorithms. RESULTS: We built an interactive visual analysis software tool (HCE2W) to test and define parameters in Affymetrix analyses that optimize the ratio of signal (desired biological variable) versus noise (confounding uncontrolled variables). Five probe set algorithms were studied with and without statistical weighting of probe sets using the MAS 5.0 probe set detection p-values. The signal-to-noise ratio optimization method was tested in two large novel microarray datasets with different levels of confounding noise, a 105 sample U133A human muscle biopsy dataset (11 groups: mutation-defined, extensive noise), and a 40 sample U74A inbred mouse lung dataset (8 groups: little noise). Performance was measured by the ability of the specific probe set algorithm, with and without detection p-value weighting, to cluster samples into the appropriate biological groups (unsupervised agglomerative clustering with F-measure values). Of the total random sampling analyses, 50% showed a highly statistically significant difference between probe set algorithms by ANOVA [F(4,10) > 14, p < 0.0001], with weighting by MAS 5.0 detection p-value showing significance in the mouse data by ANOVA [F(1,10) > 9, p < 0.013] and paired t-test [t(9) = -3.675, p = 0.005]. Probe set detection p-value weighting had the greatest positive effect on performance of dChip difference model, ProbeProfiler and RMA algorithms. Importantly, probe set algorithms did indeed perform differently depending on the specific project, most probably due to the degree of confounding noise. Our data indicate that significantly improved data analysis of mRNA profile projects can be achieved by optimizing the choice of probe set algorithm with the noise levels intrinsic to a project, with dChip difference model with MAS 5.0 detection p-value continuous weighting showing the best overall performance in both projects. Furthermore, both existing and newly developed probe set algorithms should incorporate a detection p-value weighting to improve performance. AVAILABILITY: The Hierarchical Clustering Explorer 2.0 is available at http://www.cs.umd.edu/hcil/hce/ Murine arrays (40 samples) are publicly available at the PEPR resource (http://microarray.cnmcresearch.org/pgadatatable.asp http://pepr.cnmcresearch.org Chen et al., 2004).     

Stability of molecular and rheological properties of the exopolysaccharide produced byCyanospira capsulata cultivated under different growth conditions

In order to assess the stability of molecular and rheological properties of the exopolysaccharide (EPS) produced byCyanospira capsulata the strain was cultivated under both continuous light and light-dark cycles in two culture devices, an open pond and a completely stirred reactor (CSR), having quite different surface-to-volume ratios and stirring systems. All EPS samples obtained from the cultures showed the same monosaccharidic composition and relative proportions among sugar units. However, Gel Permeation Chromatography demonstrated that EPS samples produced by cultures run in open ponds were more homogeneous in size than those obtained from cultures grown in CSR. In spite of this difference, no significant change in the flow properties was observed among the aqueous solutions of the different EPS samples.     

Incorporation of tandem mass spectrometric detection to the analysis of peptide mixtures by continuous flow fast atom bombardment mass spectrometry

The ability to acquire structurally informative daughter ion spectra for individual peptides undergoing separation and analysis by continuous flow fast atom bombardment (CF FAB) is demonstrated. To illustrate the potential of this methodology, tryptic and chymotryptic digests of the 29-residue peptide glucagon were analyzed by CF FAB using mass spectrometric and tandem mass spectrometric detection in consecutive analyses. Daughter ion spectra were recorded using B/E linked scans for the major hydrolysis products observed by liquid chromatography/mass spectrometry. The peptide mixtures were separated by gradient capillary high-performance liquid chromatography with the FAB matrix being added post-column using a coaxial flow interface between the column and flow probe. The entire effluent (3 microl min(-1)) was sampled by the mass spectrometer. Results obtained using less than 300 pmol of digested glucagon indicated several advantages to tandem mass spectrometric detection including the ability to confirm identities for products of enzymatic digestion and the potential use of this method for tandem sequence analysis of peptide mixtures.     

A small, removable microdialysis probe

A miniaturized, concentric, microdialysis probe is described. It is constructed from 36 gauge stainless steel tubing inside of 26 gauge tubing, with a cellulose hollow fiber tip 0.2 mm in diameter and 2 mm long. It has a 6000 molecular weight cut off that excludes enzymes but collects monoamines, their metabolites, and other small neurochemicals. In vitro tests show relative recovery rates of 5-10%. Absolute recovery measured in picograms was independent of the perfusate flow rate inside the probe. Tests in awake rats with probes in the nucleus accumbens showed stable amounts of catecholamines and metabolites collected during repeated 20 min samples. After ip amphetamine, release of dopamine in the accumbens increased from 20 to 40 pg per sample while DOPAC and HVA decreased from about 1500 to 500 pg. Tests of multiple site sampling succeeded in obtaining norepinephrine and dopamine plus three metabolites (DOPAC, HVA and 5HIAA) from four probes simultaneously in four different brain sites in each rat. Five day continuous samples or monthly intermittent samples can be obtained with this microdialysis probe.     

Assay of enzymatic activity by electrochemical detection of reduced coenzyme.

A highly sensitive electrochemical assay of the enzymatic activities of aqueous samples of lactate dehydrogenase, alcohol dehydrogenase, and malate dehydrogenase has been developed using an improved amperometric determination of NADH concentration in the test solution. An anode current sensitivity of 750 μA/mmol of NADH was obtained with a platinum-mesh electrode in an H cell modified to permit vigorous stirring of the anolyte. Fouling of the platinum anode was significantly decreased by working at a pH ≥ 8.1. The rate of increase in net anode current in substrate solutions containing as little as 2 × 10⁻³ unit of enzyme/ml correlated well with the rate of change in absorbance at 340 nm for each sample. The reproducibility of the assay of enzyme activity was about ± 10%.     

Molecular probe for selective detection of thiols in water of neutral pH

The ternary complex, [Zn(cyclen)(lumazine)](+) that can be readily obtained by mixing cyclen, zinc perchlorate, and lumazine in water in a 1:1:1 molar ratio serves as a molecular probe that detects selectively thiols in an aqueous solution of neutral pH. Thiols successfully displace the lumazine in the molecular probe, which is accompanied by a decrease of the fluorescence. The molecular probe is useful for identification of cysteine among essential amino acids and detection of glutathione in aqueous solution of neutral pH.     

Determination of Aconitum alkaloids in blood and urine samples. I. High-performance liquid chromatographic separation, solid-phase extraction and mass spectrometric confirmation

Determination of four toxic Aconitum alkaloids, aconitine, mesaconitine, hypaconitine and jesaconitine, in blood and urine samples has been established using high-performance liquid chromatography (HPLC) combined with ultraviolet absorbance detection, solid-phase extraction and mass spectrometry (MS). These alkaloids were hydrolyzed rapidly in alkaline solution (half lives (t_1/2)<one day), were stable in solutions of acetonitrile, tetrahydrofuran and diluted hydrochloric acid (t_1/2>five months) and were unstable in solutions of methanol and ethanol (t_1/2<one month). These alkaloids were separated on an octadecylsilica column with isocratic elution using a solvent mixture of tetrahydrofuran and 0.2% trifluoroacetic acid (14:86, v/v), which was found to be the optimal solvent of the elution systems examined. Calibration curves with UV detection were linear on injection of amounts ranging from 2.5 to 500 ng, and the limit of detection was 1 ng (S/N = 3). These four alkaloids in aqueous solution were recovered almost totally by solid-phase extraction using the styrene polymer resin, Sep-Pak Plus PS-1, and were eluted using a mixture of acetonitrile and hydrochloric acid. These Aconitum alkaloids were confirmed by HPLC coupled with fast atom bombardment MS, giving their protonated molecular ions as base peaks. These alkaloids were detected by HPLC with UV detection from blood samples spiked with more than 50 ng ml⁻¹ of alkaloids, but were not detectable from urine samples spiked with 5 μg ml⁻¹ of alkaloids because of severe sample interference.     

"Resonances" in the dielectric absorption of DNA?

An attempt was made to confirm previous reports of resonant-like dielectric absorption of plasmid DNA in aqueous solutions at 1-10 GHz. The dielectric properties of the sample were measured using an automatic network analyzer with two different techniques. One technique used an open-ended coaxial probe immersed in the sample; the other employed a coaxial transmission line. No resonances were observed that could be attributed to the sample; however, resonance-type artifacts were prominent in the probe measurements. The coaxial line technique appears to be less susceptible to such artifacts. We note two important sources of error in the calibration of the automatic network analyzer using the probe technique.     

Flow birefringence of xanthan and other polysaccharide solutions

A xanthan sample with molecular weight M = 2.2 x 10(6) was investigated in three solvents: bidistilled water, 0.2 M aqueous NaCl and cadoxen by flow birefringence and viscometry methods in dilute solutions. It was shown that the optical shear rate coefficients of xanthan in aqueous and cadoxen media differ by two orders of magnitude. An estimation of xanthan optical anisotropy in different conformational states has been made and compared with values for other polysaccharides: dextran, pullulan, cellulose and chitosan. The process of denaturation and the flow birefringence of renaturated xanthan in aqueous solutions (after heat treatment at 121 degrees C) have also been studied.     

Analysis of glycerophosphocholine molecular species as derivatives of 7-[(chlorocarbonyl)-methoxy]-4-methylcoumarin.

A method has been developed for the analysis of derivatized diradylglycerols obtained from glycerophosphocholine (GPC) of transformed murine bone marrow-derived mast cells that provided high performance liquid chromatography (HPLC) separation of GPC subclasses and molecular species separation with on-line quantitation using UV detection. In addition, the derivatized diradylglycerol species were unequivocably identified by continuous flow fast-atom bombardment mass spectrometry. GPC was initially isolated by thin-layer chromatography (TLC), the phosphocholine group was hydrolyzed, and the resultant diradylglycerol was derivatized with 7-[(chlorocarbonyl)-methoxy]-4-methylcoumarin (CMMC). After separation of the derivatized subclasses by normal phase HPLC, the individual molecular species of the alkylacyl and diacyl subclasses were quantitated and collected during a subsequent reverse phase HPLC step. With an extinction coefficient of 14,700 l mol-1 cm-1 at a wavelength detection of 320 nm, the CMMC derivatives afforded sensitive UV detection (100 pmol) and quantitation of the molecular species. Continuous flow fast-atom bombardment mass spectrometry of the alkylacyl CMMC derivatives yielded abundant [MH]+ ions and a single fragment ion formed by loss of alkylketene from the sn-2 acyl group, [MH-(R = C = O)]+. No fragmentation of the sn-1 alkyl chain was observed. Diacyl derivatives also produced abundant [MH]+ ions plus two fragment ions arising from loss of RCOOH from each of the acyl substituents and two fragment ions from the loss of alkyketene from each acyl group. Individual molecular species substituents were assigned from these ions.     

Biomolecular sample considerations essential for optimal performance from cryogenic probes

For compounds dissolved in non-polar solvents, nuclear magnetic resonance spectroscopic investigations have benefited greatly from the advent of cryogenically cooled probes. Unfortunately the allure of significant increases in sensitivity may not be realized for compounds such as metabolites that are dissolved in solvents with high ionic-strengths such as solutions typically utilized for metabolomic or biomolecular investigations. In some cases there is little benefit from a cryogenically cooled probe over a conventional room temperature probe. Various sample preparation methods have been developed to minimize the detrimental effects of salt; for large numbers of metabolomic samples these preparation methods tend to be onerous and impractical. An alternative to manipulating the sample, is to utilize a probe that is designed to have a higher tolerance for solutions with high ionic-strengths. In order to acquire high-quality optimal data and choose the appropriate probe configuration (especially important for comparative quantitative investigations) the effects of salts and buffers on cryogenic probe performance must be understood. Herein we detail sample considerations for two cryogenic probes, a standard 5 mm and a narrow diameter 1.7 mm, in an effort to identify via integrals, intensities and noise levels the optimal choice for biomolecular investigations.     

A simple preparation of half N-acetylated chitosan highly soluble in water and aqueous organic solvents

A simple and improved method of preparing highly soluble chitosan (half N-acetylated chitosan) was developed using a series of chitosan samples of low molecular weights, and the solubility of the half N-acetylated chitosan in water and organic solvents was investigated in detail. To reduce the molecular weight, chitosan was treated with NaBO3 under the condition that chitosan was homogeneously dissolved in aqueous acetic acid. Weight-average molecular weights of the obtained chitosan samples were determined using a size-exclusion chromatography system equipped with a low-angle laser light-scattering photometer. Each chitosan sample was then N-acetylated with acetic anhydride under the condition that chitosan was homogeneously dissolved in aqueous acetic acid again. The water solubility of the half N-acetylated chitosan thus prepared increased with decreasing molecular weight. From 1H NMR spectroscopy, it was suggested that the sequence of N-acetylglucosamine and glucosamine residues was random. The solubility of the half N-acetylated chitosan of low molecular weight was rather high even in aqueous dimethylacetamide and dimethylsulfoxide.     

Physicochemical characterization of konjac glucomannan

Four commercial konjac glucomannan (KGM) samples and a glucomannan derived from yeast were characterized by aqueous gel permeation chromatography coupled with multi angle laser light scattering (GPC-MALLS). Disaggregation of aqueous glucomannan solutions through controlled use of a microwave bomb facilitated reproducible molar mass distribution determination alleviating the need for derivatization of the polymer or the use of aggressive solvents. Further characterization was undertaken by use of capillary viscometry and photon correlation spectroscopy (PCS). The weight average molecular masses (M(w)) determined were in the region of 9.0 +/- 1.0 x 10(5) g mol(-1) for KGM samples and 1.3 +/- 0.4 x 10(5) g mol(-1) for the yeast glucomannan. The values determined for KGM in aqueous solution are in agreement with those reported for KGM in aqueous cadoxen. The degradation of samples observed upon autoclaving has been quantified by GPC-MALLS and intrinsic viscosity determination, allowing comparison with reported Mark-Houwink parameters. Shear flow experiments were undertaken for a range of KGM solutions of concentration 0.05 to 2.0% using a combination of controlled stress and controlled strain rheometers. The concentration dependence of the zero shear specific viscosity was determined by analysis of the data using the Ellis model. The dependence of the zero shear specific viscosity on the coil overlap parameter was defined and interpretation discussed in terms of the Martin and Tuinier equations.     

Microsequence analysis of peptides and proteins. IX. Manual gas-phase microsequencing of multiple samples

A novel apparatus for performing manual gas-phase Edman chemistry on protein and peptide samples is described. Edman chemistry is performed in 6 to 10 Teflon continuous flow reactors (CFR), previously described by J.E. Shively et al. (1987) Anal. Biochem. 163, 517-529). The CFRs are packed with 10-15 mg of Polybrene-coated spherical silica (Porasil B, Waters Associates). The gas-phase coupling reagent and cleavage reagent are 5% aqueous triethylamine and anhydrous trifluoroacetic acid, respectively, delivered by a stream of argon gas. The delivery of the gas-phase reagents is manually controlled with Hamilton 3-way valves and 2-way valves, and that of the solvents, ethyl acetate and butyl chloride, by syringe pipetting. The average cycle time is 15-20 min for 6 to 10 samples run simultaneously. Conversion of the anilinothiazolinone to phenylthiohydantoin (PTH) amino acid derivatives is accomplished manually with 25% aqueous trifluoroacetic acid. The PTH amino acids are analyzed by reversed-phase HPLC using an autosampler for handling multiple samples. Excellent results were obtained in the 100-200 pmol range. Protein samples can be sequenced from 15-20 cycles, and peptide samples usually to the COOH terminus. Initial yields ranged from 30 to 60% and repetitive yields ranged from 90 to 96%. The sample washout and size of background peaks are significantly reduced, compared to older methods of manual sequence analysis. The yields and background signal to noise are comparable to automated gas-phase Edman chemistry. The improved manual Edman described represents a low cost alternative to automated sequence analysis, and has the advantage being able to process multiple samples simultaneously.     

PFG-NMR diffusometry: a tool for investigating the structure and dynamics of noncommercial purified pig gastric mucin in a wide range of concentrations

For the first time, Pulsed Field Gradient-Nuclear Magnetic Resonance, a powerful noninvasive tool for studying the dynamics and structure of complex gels, has been used to measure diffusion of probe molecules in aqueous solutions/gels of noncommercial purified pig gastric mucin (PGM), in a concentration range up to 5 wt %. Complementary data were obtained from rheology measurements. The combination of techniques revealed a strong pH dependency of the structure of the PGM samples while changes in concentration, ionic strength, and temperature appeared to induce less pronounced alterations. Viscosity was found to vary in a nonmonotonous way with pH, with the more viscous solutions found at intermediate pH. We propose that this finding is due to a reduced charge density at lower pH, which is expected to continuously increase the relative importance of hydrophobic associations. The results suggest a loose network of expanded fully charged PGM molecules with considerable mobility at neutral pH (pH 7.4). At intermediate pH (pH 4), a three-dimensional expanded network is favored. At pH 1, the charge density is low and microphase separation occurs since hydrophobic associations prevail. This leads to the formation of clusters concentrated in PGM molecules separated by regions depleted in PGM. The results obtained increase our knowledge about the gastric mucosal layer, which in vivo contains mucin in the same concentration range as that of the samples investigated here.     

Synthesis of a highly metal-selective rhodamine-based probe and its use for the in vivo monitoring of mercury

This protocol describes detailed procedures for the preparation of a rhodamine-based mercury probe and for its applications to the detection of mercury in cells and vertebrate organisms. The mercury probe 1, which is prepared in two steps from rhodamine 6G, responds rapidly to Hg2+ in aqueous solutions with a 1:1 stoichiometry. Owing to the fact that the probe reacts with Hg2+ in an irreversible manner, it has advantages over other reversible mercury probes in in vivo assays with respect to both sensitivity and selectivity. In addition, fluorescent imaging assays of Hg2+ in live cells and zebrafish by using this mercury probe are detailed in this protocol. The approximate time frame for the preparation of the probe is 24 h and for its use in imaging assays is 1.5 h.     

SNARF-1 as an intracellular pH indicator in laser microspectrofluorometry: a critical assessment

The use of SNARF-1-AM (seminaphtorhodafluor-1-acetoxymethylester) to measure the internal pH of a single living cell by laser microspectrofluorometry has been analyzed with a lymphocyte murine B cell line A20. After incubation of the cells at 37 degrees C in the presence of 10 microM SNARF-1-AM, the internal concentration of SNARF-1 was approximately 200 microM. The enhancement of fluorescent intensity of the probe is concomitant with its leakage out of the cells. During the measurement period, this induces a continuous increase of the contribution of the external probe to the total fluorescence intensity. This prevented classical spectrofluorometry measurements, but did not preclude microspectrofluorometry measurements of internal pH. The ratio R was calculated from fluorescence intensities at 635 and 590 nm and used as an indicator of the intracellular pH. Calibration curves of the intracellular pH were obtained in the presence of nigericin and valinomycin. It appeared that both the fluorescence intensity and the ratio R were lower inside the cell than those values obtained in aqueous solutions. Possible interactions with the main biological macromolecules (i.e., DNA, proteins, membranes) were investigated as well as a possible compartmentation of the probe in cellular organelles. The modifications of probe characteristics inside the cells were attributed to the binding of the probe to cellular proteins. The intracellular pH of A20 cells, measured by SNARF-1 on 84 cells, was found to be 7.18 +/- 0.10 (with an external pH of 7.40 +/- 0.05), which corresponded with values obtained by conventional fluorometric methods.     

Asymmetrical flow field-flow fractionation enables the characterization of molecular and supramolecular properties of cereal β-glucan dispersions

In this paper we study the properties of molecular and supra molecular species in cereal β-glucan solutions/dispersions by the utilization of asymmetrical flow field-flow fractionation coupled to multi-angle light scattering and refractive index (AsFlFFF-MALS-RI) detectors. The samples were purified barley and oat β-glucans which were dissolved in aqueous solution using either mild conditions or more harsh treatments with alkali. Dissolution in 0.5 M NaOH was not sufficient to eliminate aggregated structures in barley β-glucan. The results in this paper show how distinction can possibly be made between molecular and supra molecular species using scaling approaches and conformational parameters obtained from AsFlFFF-MALS-RI over the entire size distribution. Small species in the barley β-glucan samples display properties ranging from elongated conformation to random coil conformation. Aggregates have low apparent densities and a swollen micro gel structure. Oat β-glucan displays no properties that can be attributed to a molecularly dissolved β-glucan showing that dissolution was incomplete. The aggregate properties analyzed were similar between oat and barley β-glucan.     

Determination of Herpes simplex virus DNA with the use of solid-phase methods for the detection of PCR products

To determine DNA of herpes simplex virus (HSV), types 1 and 2, the polymerase chain reaction (PCR) method was developed with the subsequent detection of amplification products by means of electrophoresis or the molecular hybridization of nucleic acids (MHNA). Two variants of MHNA have been compared: hybridization in the solution of a biotinylated probe with digoxigenin-labeled PCR with the subsequent sorption of hybridization complexes onto streptavidin-covered plates and solid-phase hybridization of digoxigenin-labeled PCR with a biotinylated probe. Effective hybridization was observed after the denaturation of targets at 95 degrees C in the solution of 50 mM NaOH, but not in neutral solutions. To increase the level of sensitivity of hybridization in solution, the exact selection of the amount of the probe was shown to be necessary, for both its excess and deficiency essentially decreased the method sensitivity. A decrease in the ionic power of hybridization solutions from 6 h SSC to 1 h SSC led to greater specificity of hybridization without a decrease in the method sensitivity. A rise in the temperature of hybridization and subsequent washing to 45 degrees C decreased the sensitivity of the method. The limit of the sensitivity PCR with electrophoretic detection was 30 HSV genome equivalents, and 10 genome equivalents in the presence MHNA in the solution and on the solid phase.