SUMMARY OF ALGORITHMIC FRAGMENTS FOR STATISTICAL IDENTIFICATION OF MARKERS FROM A SET OF SPECTRAL COURSES

A brief introduction of algorithms for the statistical identification of markers from a set of spectral courses is the topic of our paper. Partial results, demonstrated by pictures, are very promising. Therefore, our next effort will be directed at the construction of the 1st prototype of some semi-commercial software for the identification of markers from a set of spectral courses

The new platinum-based anticancer agent LA-12 induces retinol binding protein 4 in vivo

<p>Abstract</p> <p>Background</p> <p>The initial pharmacokinetic study of a new anticancer agent (<it>OC</it>-6-43)-bis(acetato)(1-adamantylamine)amminedichloroplatinum (IV) (LA-12) was complemented by proteomic screening of rat plasma. The objective of the study was to identify new LA-12 target proteins that serve as markers of LA-12 treatment, response and therapy monitoring.</p> <p>Methods</p> <p>Proteomic profiles were measured by surface-enhanced laser desorption-ionization time-of-flight mass spectrometry (SELDI-TOF MS) in 72 samples of rat plasma randomized according to LA-12 dose and time from administration. Correlation of 92 peak clusters with platinum concentration was evaluated using Spearman correlation analysis.</p> <p>Results</p> <p>We identified Retinol-binding protein 4 (RBP4) whose level correlated with LA-12 level in treated rats. Similar results were observed in randomly selected patients involved in Phase I clinical trials.</p> <p>Conclusions</p> <p>RBP4 induction is in agreement with known RBP4 regulation by amantadine and cisplatin. Since retinol metabolism is disrupted in many cancers and inversely associates with malignancy, these data identify a potential novel mechanism for the action of LA-12 and other similar anti-cancer drugs.</p

Two-dimensional quantitative near-field phase imaging using square and hexagonal interference devices

We demonstrate the formation of the near field with non-trivial phase distribution using surface plasmon interference devices, and experimental quantitative imaging of that phase with near-field phase microscopy. The phase distribution formed with a single device can be controlled by the polarization of the external illumination and the area of the device assigned to the object wave. A comparison of the experimental data to a numerical electromagnetic model and an analytical model assigns the origin of the near-field phase to the out-of-plane electric component of surface plasmon polaritons, and also verifies the predictive power of the models. We demonstrate a formation of near-field plane waves with different propagation directions on a single device, or even simultaneously at distinct areas of a single device. Our findings open the way to the imaging and tomography of phase objects in the near field

Targeted proteomics of solid cancers: from quantification of known biomarkers towards reading the digital proteome maps

<p>The concept of personalized medicine includes novel protein biomarkers that are expected to improve the early detection, diagnosis and therapy monitoring of malignant diseases. Tissues, biofluids, cell lines and xenograft models are the common sources of biomarker candidates that require verification of clinical value in independent patient cohorts. Targeted proteomics – based on selected reaction monitoring, or data extraction from data-independent acquisition based digital maps – now represents a promising mass spectrometry alternative to immunochemical methods. To date, it has been successfully used in a high number of studies answering clinical questions on solid malignancies: breast, colorectal, prostate, ovarian, endometrial, pancreatic, hepatocellular, lung, bladder and others. It plays an important role in functional proteomic experiments that include studying the role of post-translational modifications in cancer progression. This review summarizes verified biomarker candidates successfully quantified by targeted proteomics in this field and directs the readers who plan to design their own hypothesis-driven experiments to appropriate sources of methods and knowledge.</p

Intact protein profiling in breast cancer biomarker discovery: Protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry

Proteomics profiling of intact proteins based on MALDI-TOF MS and derived platforms has been used in cancer biomarker discovery studies. This approach suffers from a number of limitations such as low resolution, low sensitivity, and that no knowledge is available on the identity of the respective proteins in the discovery mode. Nevertheless, it remains the most high-throughput, untargeted mode of clinical proteomics studies to date. Here we compare key protein separation and MS techniques available for protein biomarker identification in this type of studies and define reasons of uncertainty in protein peak identity. As a result of critical data analysis, we consider 3D protein separation and identification workflows as optimal procedures. Subsequently, we present a new protocol based on 3D LC-MS/MS with top-down at high resolution that enabled the identification of HNRNP A2/B1 intact peptide as correlating with the estrogen receptor expression in breast cancer tissues. Additional development of this general concept toward next generation, top-down based protein profiling at high resolution is discussed

Proteome-wide dataset generated by iTRAQ-3DLCMS/MS technique for studying the role of FerB protein in oxidative stress in Paracoccus denitrificans

3DLC protein- and peptide-fractionation technique combined with iTRAQ-peptide labeling and Orbitrap mass spectrometry was employed to quantitate Paracoccus dentirificans total proteome with maximal coverage. This resulted in identification of 24,948 peptides representing 2627 proteins (FDR<0.01) in P. dentirificans wild type and ferB mutant strains grown in the presence or absence of methyl viologen as an oxidative stressor. The data were generated for assessment of FerB protein role in oxidative stress as published by Pernikářová et al.; proteomic responses to a methyl viologen-induced oxidative stress in the wild type and FerB mutant strains of P. denitrificans, J. Proteomics 2015;125:68–75. Dataset is supplied in the article

Non-diffracting beam synthesis used for optical trapping and delivery of sub-micron objects

ABSTRACT We demonstrate the use of interference between non-diffracting Bessel beams (BB) to generate a system of optical traps. They offer sub-micron particle confinement, delivery and organization over a distance of hundreds of µm. We analyze system of two identical counter-propagating BBs and the case of two co-propagating BBs with different propagation constants separately. In both of these cases, the interference results in periodic on-axis intensity oscillations involving particle confinement. Altering the phase of one of the interfering beams, the whole structure of optical traps can be shifted axially. Implementing this conveyor belt enables the particle delivery over the whole distance where the optical traps are strong enough for particle confinement. Experimentally we succeeded with generation of both of these systems. In case of two counter-propagating BBs we observed a strong sub-micron particle confinement, while in case of co-propagating BBs the confinement was observed only with help of fluid flow against the radiation pressure of both beams