Gas chromatographic-mass spectrometric analysis of methylphenidate and p-hydroxymethylphenidate using deuterated internal standards

A gas chromatography-mass spectrometry assay is described for the simultaneous determination of threo-dl-methylphenidate and threo-dl-p-hydroxymethylphenidate in plasma and urine using selected ion monitoring of electron impact generated fragments of their pentafluoropropionyl derivatives. The use of recently available deuterated analogues as internal standards improves overall performance relative to previous methods. The practical limit of quantifiable detection of the assay is 0.5 ng/ml for both methylphenidate and p-hydroxymethylphenidate. p-Hydroxymethylphenidate appears to be a significant urinary metabolite of methylphenidate in rats but not in humans.     

Elucidation of the initial step of oligonucleotide fragmentation in matrix-assisted laser desorption/ionization using modified nucleic acids

To probe the mechanism of gas-phase oligonucleotide ion fragmentation, modified oligonucleotides were studied using matrix-assisted laser desorption/ionization. The oligonucleotides were of the form 5'-TTTTXTTTTT, where X was a modified nucleotide. Modifications included substitution of hydroxy, methoxy, amino, and allyl groups at the 2'-position of the deoxyribose. The modified ribose contained adenine, guanine, cytosine, or uracil bases. For comparison, we studied oligomers where X was an unmodified adenosine, guanosine, cytidine, thymidine, or uridine deoxyribonucleotide. We found a very strong dependence of the matrix-to-analyte ratio on fragmentation for these oligomers. Analysis of these modifications suggests that the initial fragmentation step in MALDI-MS involves a two-step (E1) elimination of the base.     

Mismatches Improve the Performance of Strand‐Displacement Nucleic Acid Circuits

Catalytic hairpin assembly (CHA) has previously proven useful as a transduction and amplification method for nucleic acid detection. However, the two hairpin substrates in a CHA circuit can potentially react non‐specifically even in the absence of a single‐stranded catalyst, and this non‐specific background degrades the signal‐to‐noise ratio. The introduction of mismatched base pairs that impede uncatalyzed strand exchange reactions led to a significant decrease of the background signal, while only partially damping the signal in the presence of a catalyst. Various types and lengths of mismatches were assayed by fluorimetry, and in many instances, our MismatCHA designs yielded 100‐fold increased signal‐to‐background ratios compared to a ratio of 4:1 with the perfectly matched substrates. These observations could be of general utility for the design of non‐enzymatic nucleic acid circuits.     

Analysis of perfluorinated carboxylic acids in soils: detection and quantitation issues at low concentrations

Methods were developed for the extraction from soil, identification, confirmation and quantitation by LC/MS/MS of trace levels of perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA) and perfluorodecanoic acid (PFDA). Whereas PFOA, PFNA and PFDA all can be quantitated using the method of standard additions, PFOA also can be quantitated less laboriously using 13C4-PFOA as a matrix internal standard. The impact of extract matrices on signal varied between soils and temporally during analytical runs rendering 13C4-PFOA unsuitable as a matrix internal standard for quantitating perfluorinated carboxylic acids (PFCAs) other than PFOA, which co-elutes with 13C4-PFOA. In fact, for soil extracts, quantitation of PFCAs based on external calibrations proved about as accurate as use of matrix internal standards for target analytes that do not co-elute with the matrix internal standard. Also, 13C4-PFOA should be used carefully as a matrix internal standard for trace levels of PFOA because some 13C4-PFOA standards contain trace impurities of unlabelled PFOA. When the presence of PFCAs in soil extracts is being determined by LC/MS/MS, detection limits are best defined by statistical methods that quantify the significance of contrast between analytical signal and background noise using multiple analyses. Further, when developing a calibration of low concentrations using weighted regression, the central tendency of the calibration line is best fitted using graphical depictions of error. As the MDL for the transition-product quantitation ion is approached in LC/MS/MS, relatively weak signals of transition-product confirmation ions can be used as a rejection criterion by looking for anomalously high values of the ratio of the confirmation to the quantitation ion.     

The Effects of Non‐CAS Graphing Calculators on Student Achievement and Attitude Levels in Mathematics: A Meta‐Analysis

Forty‐two studies comparing students with access to graphing calculators during instruction to students who did not have access to graphing calculators during instruction are the subject of this meta‐analysis. The results on the achievement and attitude levels of students are presented. The studies evaluated cover middle and high school mathematics courses, as well as college courses through first semester calculus. When calculators were part of instruction but not testing, students' benefited from using calculators while developing the skills necessary to understand mathematics concepts. When calculators were included in testing and instruction, the procedural, conceptual, and overall achievement skills of students improved.     

Ribozyme-mediated signal augmentation on a mass-sensitive biosensor

Mass-based detection methods such as the quartz crystal microbalance (QCM) offer an attractive option to label-based methods; however the sensitivity is generally lower by comparison. In particular, low-molecular-weight analytes can be difficult to detect based on mass addition alone. In this communication, we present the use of effector-dependent ribozymes (aptazymes) as reagents for augmenting small ligand detection on a mass-sensitive device. Two distinct aptazymes were chosen: an L1-ligase-based aptazyme (L1-Rev), which is activated by a small peptide (MW approximately 2.4 kDa) from the HIV-1 Rev protein, and a hammerhead cleavase-based aptazyme (HH-theo3) activated by theophylline (MW = 180 Da). Aptazyme activity was observed in real time, and low-molecular-weight analyte detection has been successfully demonstrated with both aptazymes.     

Infrared multiphoton dissociation of small-interfering RNA anions and cations

Infrared multiphoton dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5′ P—O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for ∼25% to 40% of the product ion current, these ions were eliminated through secondary dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5′ P—O bonds began to populate the product ion mass spectra as well as higher abundances of [a − Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a − Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H]⁺, [A + H]⁺, and [C + H]⁺, which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID.     

Analysis of perfluorinated carboxylic acids in soils II: optimization of chromatography and extraction

With the objective of detecting and quantitating low concentrations of perfluorinated carboxylic acids (PFCAs), including perfluorooctanoic acid (PFOA), in soils, we compared the analytical suitability of liquid chromatography columns containing three different stationary phases, two different liquid chromatography-tandem mass spectrometry (LC/MS/MS) systems, and eight combinations of sample-extract pretreatments, extractions and cleanups on three test soils. For the columns and systems we tested, we achieved the greatest analytical sensitivity for PFCAs using a column with a C(18) stationary phase in a Waters LC/MS/MS. In this system we achieved an instrument detection limit for PFOA of 270 ag/microL, equating to about 14 fg of PFOA on-column. While an elementary acetonitrile/water extraction of soils recovers PFCAs effectively, natural soil organic matter also dissolved in the extracts commonly imparts significant noise that appears as broad, multi-nodal, asymmetric peaks that coelute with several PFCAs. The intensity and elution profile of this noise is highly variable among soils and it challenges detection of low concentrations of PFCAs by decreasing the signal-to-noise contrast. In an effort to decrease this background noise, we investigated several methods of pretreatment, extraction and cleanup, in a variety of combinations, that used alkaline and unbuffered water, acetonitrile, tetrabutylammonium hydrogen sulfate, methyl-tert-butyl ether, dispersed activated carbon and solid-phase extraction. For the combined objectives of complete recovery and minimization of background noise, we have chosen: (1) alkaline pretreatment; (2) extraction with acetonitrile/water; (3) evaporation to dryness; (4) reconstitution with tetrabutylammonium-hydrogen-sulfate ion-pairing solution; (5) ion-pair extraction to methyl-tert-butyl ether; (6) evaporation to dryness; (7) reconstitution with 60/40 acetonitrile/water (v/v); and (8) analysis by LC/MS/MS. Using this method, we detected in all three of our test soils, endogenous concentrations of all of our PFCA analytes, C(6) through C(10)-the lowest concentrations being roughly 30 pg/g of dry soil for perfluorinated hexanoic and decanoic acids in an agricultural soil.