Enhancement of protein sensitivity for MALDI imaging mass spectrometry after chemical treatment of tissue sections

MALDI imaging mass spectrometry (IMS) has become a valuable tool for the investigation of the content and distribution of molecular species in tissue specimens. Numerous methodological improvements have been made to optimize tissue section preparation and matrix deposition protocols, as well as MS data acquisition and processing. In particular for proteomic analyses, washing the tissue sections before matrix deposition has proven useful to improve spectral qualities by increasing ion yields and the number of signals observed. We systematically explore here the effects of several solvent combinations for washing tissue sections. To minimize experimental variability, all of the measurements were performed on serial sections cut from a single mouse liver tissue block. Several other key steps of the process such as matrix deposition and MS data acquisition and processing have also been automated or standardized. To assess efficacy, after each washing procedure the total ion current and number of peaks were counted from the resulting protein profiles. These results were correlated to on-tissue measurements obtained for lipids. Using similar approaches, several selected washing procedures were also tested for their ability to extend the lifetime as well as revive previously cut tissue sections. The effects of these washes on automated matrix deposition and crystallization behavior as well as their ability to preserve tissue histology were also studied. Finally, in a full-scale IMS study, these washing procedures were tested on a human renal cell carcinoma biopsy.     

Analysis of biodiesel/petroleum diesel blends with comprehensive two-dimensional gas chromatography

Comprehensive two-dimensional gas chromatography (GCxGC) is used to analyze petroleum diesel, biodiesel, and biodiesel/petroleum diesel blends. The GCxGC instrument is assembled from a conventional gas chromatograph fitted with a simple, in-line fluidic modulator. A 5% phenyl polydimethylsiloxane primary column is coupled to a polyethylene glycol secondary column. This column combination generates chromatograms where the fatty acid methyl esters (FAMEs) found in biodiesel occupy a region that is also populated by numerous cyclic alkanes and monoaromatics found in petroleum. Fortunately, the intensities of the petroleum hydrocarbon peaks are far lower than the intensities of the FAME peaks, even for blends with low biodiesel content. This allows the FAMEs to be accurately quantitated by direct integration. The method is calibrated by analyzing standard mixtures of soybean biodiesel in petroleum diesel with concentrations ranging from 1 to 20% v/v. The resulting calibration curve displays excellent linearity. This curve is used to determine the concentration of a B20 biodiesel/petroleum diesel blend obtained from a local retailer. Excellent precision and accuracy are obtained.     

Reactions of small negative ions with O2(a Δg) and O2(X Σg)

The rate constants and product ion branching ratios were measured for the reactions of various small negative ions with O₂(X ³Σ_g⁻) and O₂(a ¹Δ_g) in a selected ion flow tube (SIFT). Only NH₂⁻ and CH₃O⁻ were found to react with O₂(X) and both reactions were slow. CH₃O⁻ reacted by hydride transfer, both with and without electron detachment. NH₂⁻ formed both OH⁻, as observed previously, and O₂⁻, the latter via endothermic charge transfer. A temperature study revealed a negative temperature dependence for the former channel and Arrhenius behavior for the endothermic channel, resulting in an overall rate constant with a minimum at 500 K. SF₆⁻, SF₄⁻, SO₃⁻ and CO₃⁻ were found to react with O₂(a ¹Δ_g) with rate constants less than 10⁻¹¹ cm³ s⁻¹. NH₂⁻ reacted rapidly with O₂(a ¹Δ_g) by charge transfer. The reactions of HO₂⁻ and SO₂⁻ proceeded moderately with competition between Penning detachment and charge transfer. SO₂⁻ produced a SO₄⁻ cluster product in 2% of reactions and HO₂⁻ produced O₃⁻ in 13% of the reactions. CH₃O⁻ proceeded essentially at the collision rate by hydride transfer, again both with and without electron detachment. These results show that charge transfer to O₂(a ¹Δ_g) occurs readily if the there are no restrictions on the ion beyond the reaction thermodynamics. The SO₂⁻ and HO₂⁻ reactions with O₂(a) are the only known reactions involving Penning detachment besides the reaction with O₂⁻ studied previously [R.S. Berry, Phys. Chem. Chem. Phys., 7 (2005) 289–290].     

Early phase process scale-up challenges for fungal and filamentous bacterial cultures

Culture pelleting and morphology has a strong influence on process productivity and success for fungal and filamentous bacterial cultures. This impact is particularly evident with early phase secondary metabolite processes with limited process definition. A compilation of factors affecting filamentous or pelleting morphology described in the literature indicates potential leads for developing process-specific control methodologies. An evaluation of the factors mediating citric acid production is one example of an industrially important application of these techniques. For five model fungal and filamentous bacterial processes in an industrial fermentation pilot plant, process development strategies were developed and effectively implemented with the goal of achieving reasonable fermentation titers early in the process development cycle. Examples of approaches included the use of additives to minimize pelleting in inoculum shake flasks, the use of large-volume frozen bagged inoculum obtained from agitated seed fermentors, and variations in production medium composition and fermentor operating conditions. Results were evaluated with respect to productivity of desired secondary metabolites as well as process scalability. On-line measurements were utilized to indirectly evaluate the cultivation impact of changes in medium and process development. Key laboratory to pilot plant scale-up issues also were identified and often addressed in subsequent cultivations.     

Laser-polarized (129)Xe NMR and MRI at ultralow magnetic fields

Laser-polarized (129)Xe and a high-T(c)superconducting quantum interference device (SQUID) are used to obtain magnetic resonance images in porous materials at a magnetic field of 2.3 mT, corresponding to a Larmor frequency of 27 kHz. Image resolution of 1 mm is obtained with gradients of only 1 mT/m. The resolution of xenon chemical shifts in different physicochemical environments at ultralow fields is also demonstrated. Details of the circulating flow optical pumping apparatus and the SQUID spectrometer are presented.     

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.     

Model for predicting comprehensive two-dimensional gas chromatography retention times

A model for approximating the relative retention of solutes in comprehensive two-dimensional gas chromatography (GCxGC) is presented. The model uses retention data from standard single-column temperature-programmed separations. The one-dimensional retention times are first converted into retention indices and then these indices are combined in a simple manner to generate a retention diagram. A retention diagram is an approximation of the two-dimensional chromatogram that has retention order and spacing in both dimensions similar to that found in the experimental chromatogram. If required, the retention diagram can be scaled to more closely resemble the two-dimensional chromatogram. The model has been tested by using retention time data from single-column gas chromatography-mass spectrometry and valve-based GCxGC. A total of 139 volatile organic compounds (VOCs) were examined. Approximately half of the VOCs had a single functional group and a linear alkyl chain (i.e., compounds with the structure Z-(CH(2))(n)-H). The retention diagrams had primary retention orders that were in excellent agreement with the GCxGC chromatograms. The relative secondary retention order for compounds with similar structures was also accurately predicted by the retention diagram. However, the relative secondary retention for compounds with dissimilar structures, such as acyclic alcohols and multi-substituted alkylbenzenes, were less accurately modeled. This study demonstrates how readily available single-column retention time data can be used to provide an a priori estimate of the relative retention of solutes in a GCxGC chromatogram. Such a capability is useful for screening possible combinations of stationary phases.     

Nanostructured polymers with embedded self-assembled reactive gel networks

Generating polymers in the presence of a self-assembling gelator with terminal double bonds yields polymeric materials with embedded reactive nano-skeletons-subsequent washing gives nanoscale imprinted materials with fibrillar architectures.