Processing MALDI Mass Spectra to Improve Mass Spectral Direct Tissue Analysis

Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.     

Rapid dissolution of large environmental samples for the determination of fission products

The dissolution of large environmental samples was investigated using a microwave autoclave, capable of digestion conditions of 300 °C and 200 bar, for the application of rapid determination of radionuclides. Six samples of up to 5 g plant material were digested, also eliminating predigestion steps such as ashing and grinding. Batches of forty 1 g samples of plant leaves were also completely digested in 75 minutes. Quantitative recovery of ⁹⁰Sr from 5 g soil samples by leaching with 8M HNO₃ at 200 °C was achieved, whereas ¹³⁷Cs was not completely recovered from the large soil samples using total digestion or leaching (HCl:HNO₃) techniques, but quantitative recovery was achieved using fusion and sinter procedures.     

Friedel-Crafts reactions of 2,2-difluorocyclopropanecarbonyl chloride: unexpected ring-opening chemistry

The Friedel-Crafts reactions of 2,2-difluorocyclopropanecarbonyl chloride with various arenes did not lead to the straightforward formation of the expected aryl 2,2-difluorocyclopropyl ketones. Instead the reactions proceeded, to various degrees depending on the reactivity of the arene, via an apparent rearrangement of the initially formed acylium ion to form novel aryl 3-chloro-3,3-difluoropropyl ketones. The ring-opened product was formed exclusively, and therefore the reaction may be synthetically useful when relatively unreactive arene substrates such as benzene, toluene, and p-xylene are used. No conditions were found where ring-intact products could be formed exclusively when using substituted benzenes as substrates, with the very reactive substrate thiophene being most selective in that regard, favoring ring intact product 3 with a selectivity of 98:2. The regioselectivity of ring-opening was examined and compared with other related systems computationally.     

Conformations of laulimalide in DMSO-d6

Laulimalide is one of the newest naturally occurring macrolides known to act as a microtubule stabilizing agent with properties similar to Taxol. It also stands as being one of the most flexible with 18 rotatable bonds. This large number of rotatable bonds allows for approximately 3(18) potential conformers. To examine the conformational energy surface of laulimalide, we have performed an NAMFIS deconvolution analysis for laulimalide in DMSO-d6. The latter has been supplemented with a post-NAMFIS energy analysis at the Becke3LYP/6-31G level that examines the opposing effects of internal hydrogen bonding and syn-pentane interactions. In this way, we have identified 15 laulimalide conformations that can be classified into 5 different families: Supine, Convex, Cobra, Stretch, and Concave motifs.     

Determination of <Superscript>90</Superscript>Sr in contaminated environmental samples by tuneable bandpass dynamic reaction cell ICP–MS

A rapid method for the extraction and determination of ⁹⁰Sr in natural water, plant and sediment samples was developed using extraction chromatography and dynamic reaction cell ICP–MS, with O₂ as a reaction gas. While isobaric interference from the stable isotope ⁹⁰Zr was efficiently removed by this method, interferences produced from in-cell reactions with Fe⁺ and Ni⁺ required suppression by tuneable bandpass, and in sediments, additional chromatographic separation. Method detection limits were 0.1 pg g⁻¹ (0.5 Bq g⁻¹), 0.04 pg g⁻¹(0.2 Bq g⁻¹), and 3 pg L⁻¹ (5 Bq L⁻¹) for sediments, plant and water samples, respectively, and ⁹⁰Sr concentrations determined by ICP–MS were in good agreement with activities determined by Cerenkov counting and with certified reference values. While mass spectrometric determination does not rival detection limits achievable by radiometric counting, radiometric determination of ⁹⁰Sr, a pure beta-emitter, is hindered by long analysis times (several weeks); the comparatively fast analysis achieved via ICP–MS enables same-day preparation and analysis of samples, making this an important technique for the environmental monitoring of areas contaminated by radioactivity.     

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.     

ortho-Phenylene oligomers with terminal push-pull substitution

ortho-Phenylenes are an emerging class of helical oligomers and polymers. We have synthesized a series of push-pull-substituted o-phenylene oligomers (dimethylamino/nitro) up to the octamer. Conformational analysis of the hexamer using a combination of low-temperature NMR spectroscopy and ab initio predictions of (1)H NMR chemical shifts indicates that, like other o-phenylenes, they exist as compact helices in solution. However, the substituents are found to have a significant effect on their conformational behavior: the nitro-functionalized terminus is 3-fold more likely to twist out of the helix. Protonation of the dimethylamino group favors the helical conformer. UV/vis spectroscopy indicates that the direct charge-transfer interaction between the push-pull substituents attenuates quickly compared to other conjugated systems, with no significant charge-transfer band for oligomers longer than the trimer. On protonation of the dimethylamino group, significant bathochromic shifts with increasing oligomer length are observed: the effective conjugation length is 9 repeat units, more than twice that of the parent oligomer. This behavior may be rationalized through examination of the frontier molecular orbitals of these compounds, which exhibit greater delocalization after protonation, as shown by DFT calculations.     

Normalization in MALDI-TOF imaging datasets of proteins: practical considerations

Normalization is critically important for the proper interpretation of matrix-assisted laser desorption/ionization (MALDI) imaging datasets. The effects of the commonly used normalization techniques based on total ion count (TIC) or vector norm normalization are significant, and they are frequently beneficial. In certain cases, however, these normalization algorithms may produce misleading results and possibly lead to wrong conclusions, e.g. regarding to potential biomarker distributions. This is typical for tissues in which signals of prominent abundance are present in confined areas, such as insulin in the pancreas or β-amyloid peptides in the brain. In this work, we investigated whether normalization can be improved if dominant signals are excluded from the calculation. Because manual interaction with the data (e.g., defining the abundant signals) is not desired for routine analysis, we investigated two alternatives: normalization on the spectra noise level or on the median of signal intensities in the spectrum. Normalization on the median and the noise level was found to be significantly more robust against artifact generation compared to normalization on the TIC. Therefore, we propose to include these normalization methods in the standard “toolbox” of MALDI imaging for reliable results under conditions of automation.     

Molecular Logic Gates for DNA Analysis: Detection of Rifampin Resistance in M. tuberculosis DNA

Elementary, Dr. Watson! A combination of YES and OR logic gates was applied to differentiate between DNA sequences of wild-type and rifampin-resistant (Rif(r) ) Mycobacterium tuberculosis (Mtb) in a multiplex real-time fluorescent assay.