Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic.

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On the Nature of Mass Spectrometer Analyzer Contamination

Sample throughput in electrospray ionization mass spectrometry (ESI-MS) is limited by the need for frequent ion path cleaning to remove accumulated debris that can lead to charging and general performance degradation. Contamination of ion optics within the vacuum system is particularly problematic as routine cleaning requires additional time for cycling the vacuum pumps. Differential mobility spectrometry (DMS) can select targeted ion species for transmission, thereby reducing the total number of charged particles entering the vacuum system. In this work, we characterize the nature of instrument contamination, describe efforts to improve mass spectrometer robustness by applying DMS prefiltering to reduce contamination of the vacuum ion optics, and demonstrate the capability of DMS to extend the interval between mass spectrometer cleaning. In addition, we introduce a new approach to effectively detect large charged particles formed during the electrospray ionization (ESI) process.

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Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation

Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors that can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69% and 40% more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease.

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Methodology of chemometric modeling of spectrometric signals in the analysis of complex samples

A generalized algorithm of the multivariate simulation of spectrometric data is considered for solving typical analytical problems, like the determination of the concentration of a particular analyte and the assignment of a sample to one of predefined classes. In particular, we considered preliminary data processing, exploratory analysis, optimization of a chemometric model, calculation of performance characteristics, transfer of the model to other spectrometers, and automation of chemometric processing for the routine analysis of samples. To illustrate the potential of the method, we selected a system of bovine and porcine heparin, mixtures of soy and sunflower lecithin, and a set of red and white wine samples as test samples. Partial least squares and discriminant analysis were used as chemometric methods. We used proton nuclear magnetic resonance (1H NMR) to record signals. Using the MATLAB environment, chemometric programs were developed for automated data processing in the context of problems under consideration and for the transfer of multivariate models to other spectrometers. Based on the results obtained, a methodology is proposed for the multivariate analysis of spectrometric data, which can be used in the analysis of various types of matrices and spectrometric signals.     

Chromatographic determination of nitrophenols in aqueous media after two-stage preconcentration using an N-vinylpyrrolidone-based polymer

Two-stage procedures for the preconcentration of nitrophenols (4-nitrophenol, 2,4- and 2,5-dinitrophenol, and 2,4,6-trinitrophenol) from aqueous solutions are proposed. At the first stage, the preconcentration and desorption of nitrophenols under dynamic conditions is carried out. At the second stage, depending on the nature of the desorption solution, the eluate is evaporated (acetonitrile) or saturated with ammonium sulfate and extracted with acetone (aqueous NH₃ solution). The concentration factors are 4000 and 910, respectively. Nitrophenols are determined in concentrates by thin layer chromatography and HPLC, the limits of detection are 1.0–1.8 and 0.25–0.45 μg/L, respectively. The duration of analysis is 200 min.     

Detection and quantification of chitosan aggregates by pressure-assisted capillary zone electrophoresis

An approach to the detection and determination of chitosan aggregates in acetic acid solutions is proposed using pressure-assisted capillary zone electrophoresis. Processes of chitosan aggregation are studied depending on the composition of dispersion medium and storage time. The presence of several species of positively charged chitosan aggregates is revealed for the first time. Particle sizes in the range 20–2500 nm are determined by scanning electron microscopy and static and dynamic light scattering. The dependence of the shape of electropherograms on particle size distribution obtained under the same conditions is found. A trend to changing electrophoretic mobility depending on the size of the aggregate is observed, which enables the approximate evaluation of the polydispersity of chitosan solutions. Chitosan is used for the effective dynamic modification of capillaries, which does not require the introduction of a modifier into the background electrolyte.     

Determination of the surface area of loose metal deposits by impedance spectroscopy

The surface area and fractal dimensions of the surface of loose copper and zinc deposits obtained within 30 and 300 s at direct current sixfold exceeding limiting diffusion current on a smooth electrode were in situ determined by impedance spectroscopy. Impedance measurements were performed in 0.5 M Na₂SO₄ solution. A constant phase element taking into account the distribution of double-layer capacitance over the fractal surface of the electrode was used in the equivalent impedance scheme. Specific surface calculated with regard to the weight of the released metal slightly varied within 300 s (from 6.16 to 6.55 and from 7.12 to 5.89 m²/g for copper and zinc deposits, respectively). Fractal dimensions estimated by chronopotentiometry were given for comparison. Fractal dimensions found by two methods for loose copper and zinc deposits agree with each other; their values (2.19–2.75) testify that the surface of the deposits densely fills the space.     

An electrochemical aptasensor for cytochrome C,based on pillar[5]arene modified with Neutral Red

An electrochemical aptasensor is developed for the highly sensitive determination of cytochrome C, using a change in the redox current of Neutral Red covalently bound to terminal carboxyl groups of decasubstituted pillar[5]arene as a signal. The inclusion of the analyte into the complex with an aptamer reduces peaks of redox current of the dye through the dissociation of electron transfer chain in the surface layer. The aptasensor enables the determination of 1 nM to 1.0 mM of cytochrome C in the presence of 1000-fold excesses of albumin, polyethylene glycol, and lysozyme as models of interfering components in biological fluids.     

Mechanism of reaction of selenium elimination in diacetophenonyl selenide under the action of reduced glutathione

Products of reaction between the organoselenium xenobiotic, diacetophenonyl selenide (1,5-diphenyl-3-selenapenta-1,5-dione), and reduced glutathione at different molar ratios and pH values were studied by HPLC and TLC. Reaction intermediates, S-(acetophenylselenyl)glutathione and glutathione selenodisulfide, and reaction products, acetophenone and hydroselenide anion, were detected. The reaction scheme proposed earlier was confirmed.     

A New Approach to Increasing the Resolution of a Mass Spectrometer with Wedge-Shaped Reflectors

The paper describes the investigation of the ion-optical properties of a laser TOF mass spectrometer including two successively positioned wedge-shaped ion mirrors. Some specific properties of the configuration of ion trajectories near their reflection in the second ion reflector are found. The dependence of aberrations on ion energy acquired toothed shape for the resolution of the analyzer higher than 3000–5000. The approximation of the dependence gave a 15^th degree polynomial. The calculation of polynomial coefficients showed a great contribution to the duration of ion packets for aberrations of higher order. The discovered features allowed us to suggest a way of the local correction of nearby trajectories in the total ion flux. By correcting the local motion of individual groups of ions, we could reduce temporary aberration to 1–1.6 ns, depending on ion energy. For the time of ion flight ~35 μs, such duration limits the resolution of the analyzer by a value not less than 10000. The real length of ion drift path was about 30 cm. The total overall sizes of the ionoptical system were ~24 × 19 × 5 cm.