Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

Investigation of the quantitative properties of the quadrupole orthogonal acceleration time-of-flight mass spectrometer with electrospray ionisation using 3,4-methylenedioxymethamphetamine

This paper describes the investigation of the potential of a quadrupole orthogonal acceleration time-of-flight mass spectrometer (Q-TOF) equipped with an atmospheric pressure ionisation interface for quantitative measurements of small molecules separated by reversed phase liquid chromatography. To this end, the detection limits and linear dynamic range in particular were studied in an LC/MS/MS experiment using 3,4-methylenedioxymethamphetamine standards and 3,4-methylenedioxyethylamphetamine for internal standardisation. In a second phase, the experiment was repeated with real biological extracts (whole blood, serum, and vitreous humour). A calibration for 3,4-methylenedioxymethamphetamine and its metabolite 3,4-methylenedioxyamphetamine was prepared in each of these matrices again using 3,4-methylenedioxyethylamphetamine as internal standard. The resulting quantitative data were compared with those obtained by liquid chromatography with fluorescence detection for the same extracts. The Q-TOF results revealed excellent sensitivity and a linear dynamic range of nearly four decades (2-10 000 pg on-column, r(2) = 0.9998, 1/x weighting). Furthermore, all the calibration curves prepared in biological material were superimposable, LC/MS/MS and LC-fluorescence, and the quantitative results for actual samples compared very favourably. It was concluded that the Q-TOF achieves a linear dynamic range for quantitative LC/MS/MS work exceeding that of fluorescence detection and at much better absolute sensitivity. Copyright 1999 John Wiley & Sons, Ltd.     

Supercritical hydrogen adsorption in nanostructured solids with hydrogen density variation in pores

Experimental excess isotherms for the adsorption of gases in porous solids may be represented by mathematical models that incorporate the total amount of gas within a pore, a quantity which cannot easily be found experimentally but which is important for calculations for many applications, including adsorptive storage. A model that is currently used for hydrogen adsorption in porous solids has been improved to include a more realistic density profile of the gas within the pore, and allows calculation of the total amount of adsorbent. A comparison has been made between different Type I isotherm equations embedded in the model, by examining the quality of the fits to hydrogen isotherms for six different nanoporous materials. A new Type I isotherm equation which has not previously been reported in the literature, the Unilan-b equation, has been derived and has also been included in this comparison study. These results indicate that while some Type I isotherm equations fit certain types of materials better than others, the T?th equation produces the best overall quality of fit and also provides realistic parameter values when used to analyse hydrogen sorption data for a model carbon adsorbent.     

Isosteric enthalpies for hydrogen adsorbed on nanoporous materials at high pressures

A sound understanding of any sorption system requires an accurate determination of the enthalpy of adsorption. This is a fundamental thermodynamic quantity that can be determined from experimental sorption data and its correct calculation is extremely important for heat management in adsorptive gas storage applications. It is especially relevant for hydrogen storage, where porous adsorptive storage is regarded as a competing alternative to more mature storage methods such as liquid hydrogen and compressed gas. Among the most common methods to calculate isosteric enthalpies in the literature are the virial equation and the Clausius–Clapeyron equation. Both methods have drawbacks, for example, the arbitrary number of terms in the virial equation and the assumption of ideal gas behaviour in the Clausius–Clapeyron equation. Although some researchers have calculated isosteric enthalpies of adsorption using excess amounts adsorbed, it is arguably more relevant to applications and may also be more thermodynamically consistent to use absolute amounts adsorbed, since the Gibbs excess is a partition, not a thermodynamic phase. In this paper the isosteric enthalpies of adsorption are calculated using the virial, Clausius–Clapeyron and Clapeyron equations from hydrogen sorption data for two materials—activated carbon AX-21 and metal-organic framework MIL-101. It is shown for these two example materials that the Clausius–Clapeyron equation can only be used at low coverage, since hydrogen’s behaviour deviates from ideal at high pressures. The use of the virial equation for isosteric enthalpies is shown to require care, since it is highly dependent on selecting an appropriate number of parameters. A systematic study on the use of different parameters for the virial was performed and it was shown that, for the AX-21 case, the Clausius–Clapeyron seems to give better approximations to the exact isosteric enthalpies calculated using the Clapeyron equation than the virial equation with 10 variable parameters.     

Repeatability and reproducibility of determination of the nitrogen content of fishmeal by the combustion (Dumas) method and comparison with the Kjeldahl method: interlaboratory study

Ten fishmeal samples (hidden duplicates of 4 meals plus 2 high-protein meals as a Youden pair), tryptophan, and nicotinic acid were analyzed by 18 laboratories using the Dumas method. Thirteen of the laboratories also analyzed the same 12 samples using their current Kjeldahl method. Recoveries (+/-SR) of tryptophan and nicotinic acid were 99.3+/-1.04 and 98.8+/-2.11% by Dumas and 97.1+/-3.03 and 74.6+/-26.76% by Kjeldahl. The Dumas method gave significantly greater values (P < 0.001) than the Kjeldahl method. For fishmeals, Kjeldahl N = 0.989 of Dumas N (P < 0.001). A similar proportionate difference (0.984 of Dumas N) was observed with tryptophan. Most laboratories failed to determine nicotinic acid correctly by Kjeldahl. For fishmeals, the relative standard deviations for repeatability and reproducibility were for Dumas 1.48 and 2.01% and Kjeldahl 1.62 and 2.37%, respectively. A single analysis conducted in 2 laboratories should not differ by more than 5.63% of the mean value when measured by Dumas or by more than 6.64% by Kjeldahl. It is concluded that with fishmeal, Dumas gives a more reliable measure of organic nitrogen than Kjeldahl, and, therefore, Dumas should be the method of choice.     

Determination of nitrogen solubility in dilute pepsin hydrochloric acid solution of fishmeal: interlaboratory study

A revised method to determine solubility of nitrogen in dilute pepsin, using 0.0002% pepsin in place of 0.2% in AOAC Official Method 971.09, was tested in 16 laboratories with 12 samples of fishmeal. Results were calculated according to 2 procedures: AOAC Official Method 971.09 and a method described in 1964 by researchers at the Torry Research Station (Aberdeen, Scotland), and generally referred to as the modified Torry method. Variations in the method of shaking and source of pepsin were also investigated. Pepsin solubility values were lower and more variable when calculated by the Torry procedure. The method of shaking apparently affected the result when calculated according to the Torry but not the AOAC method. The source of pepsin had no significant effect on between-laboratory variability, but a comparison of the 2 main sources within one laboratory resulted in highly significant differences. Based on this study, the International Fishmeal and Fish Oil Organization has adopted this new method, using 0.0002% pepsin but keeping the AOAC method of calculation. The type of shaker and source of pepsin are recommended but are not mandatory. The repeatability and reproducibility limits of this new method are 1.6 and 3.3% units of solubility, respectively.     

Working group report: Heavy-ion physics and quark-gluon plasma

This is the report of Heavy Ion Physics and Quark-Gluon Plasma at WHEPP-09 which was part of Working Group-4. Discussion and work on some aspects of quark-gluon plasma believed to have created in heavy-ion collisions and in early Universe are reported.     

Quantum space-times in the year 2002

We review certain emergent notions on the nature of space-time from noncommutative geometry and their radical implications. These ideas of space-time are suggested from developments in fuzzy physics, string theory, and deformation quantization. The review focuses on the ideas coming from fuzzy physics. We find models of quantum space-time like fuzzy S ⁴ on which states cannot be localized, but which fluctuate into other manifolds like CP³. New uncertainty principles concerning such lack of localizability on quantum space-times are formulated. Such investigations show the possibility of formulating and answering questions like the probability of finding a point of a quantum manifold in a state localized on another one. Additional striking possibilities indicated by these developments is the (generic) failure of CPT theorem and the conventional spin-statistics connection. They even suggest that Planck’s ‘constant’ may not be a constant, but an operator which does not commute with all observables. All these novel possibilities arise within the rules of conventional quantum physics, and with no serious input from gravity physics.