Evaluation of different two‐dimensional chromatographic techniques for proteomic analysis of mouse cardiac tissue

In proteomics experiments the first critical step after sampling is certainly sample preparation. Multidimensional chromatography techniques have emerged as a powerful tool for the large‐scale analysis of such complex samples as biological samples. In order to evaluate these separation techniques, microgram quantities of protein extracted from mouse heart tissue were fractionated by four different chromatographic methods. Regarding peptide‐level fractionation, the first dimension of separation was performed with high‐pH reversed‐phase chromatography (pH‐RP) and strong cation exchange chromatography (SCX). Regarding protein‐level fractionation, C₈ protein reversed‐phase (C₈‐RP Prot) and high‐recovery protein reversed‐phase (hr‐RP Prot) were used instead. The second dimension consisted of a reversed‐phase nano‐HPLC on‐Chip coupled to an electrospray ionization quadrupole time‐of‐flight mass spectrometer for tandem mass spectrometric analysis. The performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The peptide‐level pH‐RP and the hr‐RP Prot protein‐level separations were the best methods, identifying 1338 and 1303 proteins, respectively. The peptide‐level SCX, with 509 proteins identified, was the worst method. Copyright © 2010 John Wiley & Sons, Ltd.     

On the Lebesgue decomposition for non-additive functions

A Lebesgue decomposition theorem for non-additive functions, acting on a \(\sigma \) -complete orthomodular lattice and taking values in Hausdorff uniform spaces, is established. No algebraic structure is required on target spaces. The Boolean case is also investigated.     

Absolute quantification of cardiac troponin T by means of liquid chromatography/triple quadrupole tandem mass spectrometry

A liquid chromatography/tandem mass spectrometric method for absolute quantification of cardiac troponin T (cTnT) in mouse heart tissue is presented. Even in such a complex biological sample, the multiple reaction monitoring acquisition mode allowed the selective and sensitive determination of a specific peptide, obtained by cTnT enzymatic digestion. The concentration of this cTnT-specific peptide was considered as a representation of the concentration of its parent protein. Quantification was carried out by means of the matrix-matched calibration curve, constructed by adding the synthetic standard of the target peptide and another synthetic structurally analogous peptide as internal standard. Method identification limit and method quantification limit were estimated as 60 and 110 ng of cTnT per mg of total extracted proteins, respectively. The developed label-free approach has been applied for the absolute quantitation of cTnT because of its diagnostic and prognostic value as cardiac disease marker. However, the method could be of general application, since it requires only the synthesis of two suitable peptides, a protein tryptic cleavage product and an internal standard.     

Identification of changes in <Emphasis Type="Italic">Triticum durum</Emphasis> L. leaf proteome in response to salt stress by two-dimensional electrophoresis and MALDI-TOF mass spectrometry

In order to understand the molecular basis of salt stress response, a proteomic approach, employing two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), was used to identify proteins affected by salinity in wheat (Triticum durum ‘Ofanto’). Identification of proteins, whose levels were altered, was performed by comparing protein patterns of salt-treated and control plants. A set of control plants was grown without NaCl addition under the same conditions as the salt-treated plants. Proteins were extracted from the leaves of untreated and NaCl-treated plants, and resolved using 24-cm immobilized pH gradient strips with a pH 4–7 linear gradient in the first dimension and a 12.5% sodium dodecyl sulphate polyacrylamide gel electrophoresis in the second dimension; the gels were stained with Coomassie and image analysis was performed. Quantitative evaluation, statistical analyses and MALDI-TOF MS characterization of the resolved spots in treated and untreated samples enabled us to identify 38 proteins whose levels were altered in response to salt stress. In particular, ten proteins were downregulated and 28 were upregulated. A possible role of these proteins in response to salinity is discussed.     

Phosphopeptide enrichment: Development of magnetic solid phase extraction method based on polydopamine coating and Ti-IMAC

Protein post translational modifications currently represent one of the main challenges with proteomic analysis, due to the important biological role they play within cells. Protein phosphorylation is one of the most important, with several approaches developed for phosphopeptides enrichment and analysis, essential for comprehensive phosphoproteomic analysis. However, the development of new materials for phosphopeptides enrichment may overcome previous drawbacks and improve enrichment of such peptides. In this regard, new magnetic stationary phases based on polydopamine coating and Ti⁴⁺ immobilization exploit the potential of IMAC enrichment and couple it with the versatility of magnetic solid phase extraction. In this work the use of such stationary phase was extended from the MALDI proof of concept stage with the development of an optimized method for phosphopeptides enrichment compatible with typical shotgun proteomics experimental workflows. Different loading and elution buffers were tested to improve phosphopeptides recovery and enrichment selectivity. Finally, the analysis of isolated peptides pointed out that polydopamine alone is an ideal support matrix for polar post translational modifications because it enables to reduce unspecific binding and preferentially binds hydrophilic peptides.     

Sarcosine as a marker in prostate cancer progression: a rapid and simple method for its quantification in human urine by solid-phase microextraction–gas chromatography–triple quadrupole mass spectrometry

Sarcosine is an amino acid derivative of N-methylglycine and is involved in the amino acid metabolism and methylation processes that are enriched during prostate cancer progression. It could also serve as a new target to be measured during therapeutic interventions and help in the identification of aggressive tumors for radical treatment. In this study, we present a new urine test that can help early diagnosis of prostate cancer. The method for the quantification of sarcosine in urine consists of a solid-phase microextraction (SPME) step followed by gas chromatography–triple quadrupole mass spectrometry analysis. We used a preliminary derivatization step with ethyl chloroformate/ethanol and the corresponding ester was then extracted by SPME in immersion mode. Several fibers were evaluated and the optimization of the parameters affecting the SPME process was carried out using an experimental design. The optimal values were 20 min extraction time, 10% NaCl, and 270°C using a divinylbenzene/Carboxen/polydimethylsiloxane fiber. The triple quadrupole analyzer acquired data in selected reaction monitoring mode, allowing us to obtain reconstructed chromatograms with well-defined chromatographic peaks. The accuracy and precision of this method were evaluated at concentrations of 70, 250, and 800 ng/ml and were found to be acceptable. Very satisfactory values (0.10 and 0.16 ng/ml, respectively) were also achieved for the limit of detection and the limit of quantification. The proposed protocol represents a rapid, simple, selective, and sensitive tool to quantify sarcosine in urine samples for prostate cancer diagnosis and for a screening test.     

A Comparison of the Blow-Off Behaviour of Swirl-Stabilized Premixed, Non-Premixed and Spray Flames

Confined short turbulent swirling premixed and non-premixed methane and heptane spray flames stabilized on an axisymmetric bluff body in a square enclosure have been examined close to the blow-off limit and during the extinction transient with OH* chemiluminescence and OH-PLIF operated at 5 kHz. The comparison of flames of different canonical types in the same basic aerodynamic field allows insights on the relative blow-off behaviour. The flame structure has been examined for conditions increasingly closer to blow-off. The premixed flame was seen to change from a cylindrical shape at stable burning condtions, with the flame brush closing across the flow at conditions close to blow-off. The PLIF images show that for the gaseous non-premixed flame, holes appear along the flame sheet with increasing frequency as the blow-off condition is approached, while the trend is less obvious for the spray flame. Non-premixed and spray flames showed randomly-occurring lift-off, which is further evidence of localised extinction. The mean lift-off height increased with increasing fuel jet velocity and decreased with increasing air velocity and approaches zero (i.e. the flame is virtually attached) just before the blow-off condition, despite the fact that more holes were evident in the flame sheet as extinction was approached. It was found that the average duration of the blow-off event, when normalised with the characteristic flow time d/U _b (d being the bluff-body diameter and U _b the bulk velocity) was in the range 9–38 with the spray flame extinction lasting a shorter time than the gaseous flames. Finally, it was found that correlations based on a Damköhler number collapse the blow-off velocity data for all flames with reasonable accuracy. The results can help the development of advanced turbulent combustion models.     

Characterization of the Trans-Epithelial Transport of Green Tea (C. sinensis) Catechin Extracts with In Vitro Inhibitory Effect against the SARS-CoV-2 Papain-like Protease Activity

This work describes an untargeted analytical approach for the screening, identification, and characterization of the trans-epithelial transport of green tea (Camellia sinensis) catechin extracts with in vitro inhibitory effect against the SARS-CoV-2 papain-like protease (PLpro) activity. After specific catechin extraction, a chromatographic separation obtained six fractions were carried out. The fractions were assessed in vitro against the PLpro target. Fraction 5 showed the highest inhibitory activity against the SARS-CoV-2 PLpro (IC₅₀ of 0.125 μg mL⁻¹). The untargeted characterization revealed that (−)-epicatechin-3-gallate (ECG) was the most abundant compound in the fraction and the primary molecule absorbed by differentiated Caco-2 cells. Results indicated that fraction 5 was approximately 10 times more active than ECG (IC₅₀ value equal to 11.62 ± 0.47 μg mL⁻¹) to inhibit the PLpro target. Overall, our findings highlight the synergistic effects of the various components of the crude extract compared to isolated ECG.     

Laser-Assisted particle-atom inelastic collisions. Role of the field polarization

Summary A theoretical treatment, of first order in the collision dynamics, is presented to analyse the role of electric polarization in offresonance laser-assisted atomic collisions. General expressions are presented for evaluating the modified spectrum and wave functions for anyn level of hydrogenic atoms in the presence of a laser, taken to be linearly and circularly polarized. Specific calculations are carried out for excitation of hydrogen atoms to the leveln=2 by electron impact. The two polarizations are found to yield large differences i) in the atomic-spectrum modifications, ii) in the structure of the cross-sections and iii) in the numerical results. In particular, only for linear polarization, the distribution in energy of the scattered electrons at a fixed scattering angle has the structure of a series of equally spaced lines of different height (the spacing being equal to the laser photon energy ℏw and the height of the line accounting for the number of final electrons with a given energy). For circular polarization no such a regular pattern is predicted. Since, among laser-assisted particle-atom collisions, at present energy gain-loss spectra of scattered electrons are most easily observed, it is hoped that the reported results may serve as a stimulus for new observations in this new class of atomic collisions. The theory to treat the multiphoton resonance case is outlined too. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.