The software for interactive evaluation of mass spectra stability and reproducibility.

SUMMARY: Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here, we present spectra similarity matrix (SSM) Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra. AVAILABILITY AND IMPLEMENTATION: Source code, example datasets, binaries and other information are available at https://github.com/EvgenyZhvansky/R_matrix. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Endoparasites of Wild Boars (Sus Scrofa) in Primorsky Krai, Russia.

This study identified helminthic species among wild boars (Sus scrofa) in Primorsky Krai, Russia. In total, 66 fecal samples were taken from wild boars and examined using the floatation-sedimentation method to identify helminths eggs and protozoan cysts. Age and sex were estimated for each host animal investigated. The helminthic fauna of the wild boars examined involved six parasite genera, but 4 are helminths and 2 are protozoans: the nematodes Metastrongylus spp., Trichuris suis, Capillaria sp. and Ascaris suum; and the protozoan parasites Eimeria sp. and Cystoisospora suis. The most prevalent parasite was Metastrongylus spp. (13.6 %) followed by Trichuris suis (7.6 %). The other parasites found were Eimeria sp. (3 %), Ascaris suum (3 %), Capillaria sp. (1.5 %) and Cystoisospora suis (1.5 %). Not found positive correlation between the host's age and sex and the parasite prevalence. This was the first detailed study on helminths infections among wild boars in Primorsky Krai.

[The role of lipid metabolism disorders, atypical isoforms of protein kinase C, and mutational status of cytosolic and mitochondrial forms of isocitrate dehydrogenase in carcinogenesis of glial tumors]. / Rol' narushenii lipidnogo obmena, atipicheskikh izoform proteinkinazy S i mutatsionnogo statusa tsitozol'noi i mitokhondrial'noi form izotsitratdegidrogenazy v kantserogeneze glial'nykh opukholei.

The relationship between molecular genetic and metabolic disorders is one of the challenges of modern oncology. In this review, we consider lipid metabolism and its changes as one of the factors of oncogenesis of glial tumors. Also, we demonstrate that the genome and the metabolome are interconnected by a large number of links, and the metabolic pathways, during their reorganization, are able to drastically affect the genetic structure of the cell and, in particular, cause its tumor transformation. Our own observations and analysis of the literature data allow us to conclude that mass spectrometry is a highly accurate current method for assessing metabolic disorders at the cellular level. The use of mass spectrometry during surgery allows the neurosurgeon to obtain real-time data on the level of specific molecular markers in the resected tissue, thereby bringing intraoperative navigation techniques to the molecular level. The generation of molecular fingerprints for each tumor significantly complements the available neuroimaging, molecular genetic, and immunohistochemical data.

High-resolution mass spectra processing for the identification of different pathological tissue types of brain tumors.

The purpose of the work is to demonstrate the possibilities of identifying the different types of pathological tissue identification directly through tissue mass spectrometry. Glioblastoma parts dissected during neurosurgical operation were investigated. Tumor fragments were investigated by the immunohistochemistry method and were identified as necrotic tissue with necrotized vessels, necrotic tissue with tumor stain, tumor with necrosis (tumor tissue as major), tumor, necrotized tumor (necrotic tissues as major), parts of tumor cells, boundary brain tissue, and brain tissue hyperplasia. The technique of classification of tumor tissues based on mass spectrometric profile data processing is suggested in this paper. Classifiers dividing the researched sample to the corresponding tissue type were created as a result of the processing. Classifiers of necrotic and tumor tissues are shown to yield a combined result when the tissue is heterogeneous and consists of both tumor cells and necrotic tissue.

Label-free study of cosmonaut's urinary proteome changes after long-duration spaceflights.

During the entire time that cosmonauts stay on board the international space station, different extreme space flight factors affect their bodies. In order to find out what physiological changes occur under the influence of spaceflight, different parameters of the human body before and after flights are monitored. Analysis of the urine proteome is one of the most perspective non-invasive methods of condition monitoring. The aim of the study was to perform a comparative semi-quantitative label-free urine proteome analysis of samples collected from 21 cosmonauts before and after long-duration spaceflight at the international space station. For proteomic analysis, urine samples were collected from cosmonauts at three time periods: six months prior to the flight as a background, and on days 1 and 7 of the recovery period after landing. All probes were analyzed by LC-MS/MS, and 256 proteins were identified with more than one unique peptide. The core proteome consists of 50 proteins that are detected in more than 70% of the samples. Label-free semi-quantitative analysis enables us to find 20 proteins which were significantly changed on +1 day and +7 day with respect to background. Most of these proteins participate in the regulation of biological processes, in the regulation of the immune system and in intracellular processes also; some of these proteins are related with stress and response to stimulus. In conclusion, the proteomic analysis of cosmonauts' urine samples provides new data on the human body's adaptation to ground conditions after long-duration spaceflight.

Evaluation of plasma peptides extraction methods by high-resolution mass spectrometry.

Monitoring of peptides offers a promising approach for the discovery of novel biomarkers, which might be valuable for detection, treatment and prevention of large variety of diseases. Development of highly effective methods for plasma peptide extraction remains an important task. In the current study, we applied different types of plasma peptide extraction approaches to reveal efficient methods which would provide the highest peptide yield. We used different combinations of plasma treatment with acetonitrile and/or urea/guanidine, protein precipitation by acetone, gel-filtration, ultrafiltration, and two types of solid phase extraction. The extracted peptides were analyzed by LC-MS/MS. The obtained results suggest that several methods, including differential solubilization, organic precipitation, as well as some variants of ultrafiltration and solid phase extraction, provide effective plasma peptide enrichment convenient for further LC-MS/MS analysis. Alas, most of the identified peptides were extracted by only one of the applied methods. Hence, it seems reasonable to consider several methods to increase the possibility of novel biomarker discovery.

[Secondary Structure of Aß(1-16) Complexes with Zinc: A Study in the Gas Phase Using Deuterium/Hydrogen Exchange and Ultra-High-Resolution Mass Spectrometry].

Complexes of peptide fragment 1-16 of beta-amyloid with transition metals play an important role in the development of a broad class of neurodegenerative diseases, which determines the interest in investigating the structures of these complexes. In this work, we have applied the method of the deuterium/hydrogen exchange in combination with ultra-high-resolution mass spectrometry to study conformational changes in (1-16) beta-amyloid peptide induced by binding of zinc(II) atoms. The efficiency of the deuterium/hydrogen exchange depended on the number of zinc atoms bound to the peptide and on the temperature of the ionization source region. Deuterium/hydrogen exchange reactions have been performed directly in the ionization source. The number of exchanges decreased considerably with an increasing numbers of zinc atoms. The relationship has been described with a damped exponential curve, which indicated that the binding of zinc atoms altered the conformation of the peptide ion by making it less open, which limits the access to inner areas of the molecule.

[Determination of proteomic and metabolic composition of exhaled breath condensate of newborns].

Here, the possibility of proteomic and metabolomic analysis of the composition of exhaled breath condensate of neonates with respiratory support. The developed method allows non-invasive collecting sufficient amount of the material for identification of disease-specific biomarkers. Samples were collected by using a condensing device that was incorporated into the ventilation system. The collected condensate was analyzed by liquid chromatography coupled with high resolution mass spectrometry and tandem mass spectrometry. The isolated substances were identified with a use of databases for proteins and metabolites. As a result, a number of compounds that compose the exhaled breath condensate was determined and can be considered as possible biomarkers of newborn diseases or stage of development.

Studying the Proteomic Composition of Expired Air Condensate in Newborns on Breathing Support.

This study was designed to collect and perform a proteomic analysis of expired air condensate in newborns receiving respiratory support at the Department of Resuscitation and Intensive Care. The proteomic composition of expired air condensate was evaluated in newborns at various stages of development and with different abnormalities.

Proteomic Analysis of the Urine for Diagnostics in Newborns.

Proteomic analysis of the urine was used for noninvasive diagnostics of abnormalities in newborns treated in the neonatal intensive care unit. This approach can be used to differentiate between infectious and noninfectious respiratory disorders.

[Urine proteome study for the evaluation of age dynamics in healthy men].

We investigated the age dynamics of proteomic profile of urine in 52 healthy men aged 18 to 51 years. A special sample preparation was performed, followed by liquid chromatography-mass spectrometry. Liquid chromatography-mass spectrometry of the minor proteins was performed on a nano-HPLC Agilent 1100 system («Agilent Technologies Inc.¼, USA) in combination with a LTQ-FT Ultra mass spectrometer («Thermo Electron¼, Germany). A total of 259 proteins were identified. According to the TiGER database, a tissue origin was established for 141 proteins and identified 715 processes in which they participate. We found a significant positive correlation with age, the number of proteins (R=0,566; p-value=1,24E-05) and the weight of proteins (R=0,45; p value=8,17E-04). Identified 23 proteins were significantly more frequent in the urine of subjects with increasing age (p<0,05), and only one protein - RGSL, Regulator of G protein signaling protein-like (MW 125.69) - less frequently.

[Estimation of phosphorilation level of amyloid beta, extracted from human blood plasma. Ultra high resolution mass spectrometry].

Recently it has been shown that phosphorylation of the Ser8 residue in amyloid-beta (pS8-Abeta) is tightly involved in the pathogenesis ofAlzheimer's disease. Since this modification occurs in the key metal-binding domain of amyloid-beta, and thus should seriously affect the interaction of pS8-Abeta with zinc ions, this isoform might be a potential precursor of pathogenic oligomeric forms of amyloid beta. Hence the level of pS8-Abeta in human biological fluids (such as blood, urine, cerebral spinal fluid) might resemble the different stages of the pathogenesis of Alzhe- imer's disease. The aim of this workwas to develop a prototype of an analytical method for quantitative determination of the level of pS8-Abeta isoform in binary mixtures with native amyloid-beta in order to further use it to determine the levels of phosphorylated amyloid-beta in blood plasma samples of patients with Alzheimer's disease.

[Permanent proteins in healthy human's urine in the experiment with 520-day isolation].

Purpose of the study was to track permanent proteins of urine proteome in the 520-day isolation experiment at the IBMP Ground-Based Test Facility with controlled environmental parameters. Object of the investigation was urine sampled from 6 normal male subjects at the age of 25 to 37 years. Second morning aliquots were gathered during baseline data collection, on days 50, 93, 124, 153, 180, 251, 274, 303, 330, 371, 400 and 427 of isolation, and in 7 days after its completion. Samples were subject to chromatography-mass spectrometry; results were analyzed with the help of bioinformatics resources. The following 7 permanent proteins were observed in urine over the entire length of the investigation: epidermal growth factor, polymer immunoglobulin receptor, plasma serine protease inhibitor, protein AMBP, keratin, type II cytoskeletal 1, collagen alpha-1 (vi) chain, serum albumin.

[Identification of the minimal zinc-binding center in natural isoforms of amyloid-beta domain 1-16 using ESI-MS].

Alzheimer's disease, is a lethal neurodegenerative pathology, characterized by the formation of soluble neurotoxic oligomers of the human amyloid-beta peptide Abeta which get accumulated forming polymeric extracellular aggregates (so-called amyloid plaques). The isomerized at aspartate 7 isoform of the human Abeta (isoAbeta) is the main component of these plaques and is considered as the potential pathogenic agent of AD. Besides this, there is a possible generation mechanism for this isoform from a genetically deficient D7N Abeta variant (Tottori mutation). On the contrary the rodent Abeta (rat Abeta), which has three amino acid substitutions in its metal-binding domain, is not susceptible to pathogenic aggregation in vivo, unlike the other known natural isoforms of Abeta. Interactions with zinc ions play a crucial role in the aggregation of monomeric human Abeta in vitro and in vivo. In the presented article using high resolution ESI-MS methods it was shown that domains 1-16 of isoAbeta and D7NAbeta bind zinc ions in the exactly the same manner as the normal human Abeta1-16, whereas ratAbeta has significant differences in structure of its minimal zinc binding center. These results confirm the overall interaction mechanism between zinc ions and the humanAbeta isoforms and allows to suppose that perhaps modulation of the structure of region 6-14 of Abeta can be used as a promising therapeutic approach to AD treatment.

[Identification of transthyretin posttranslational modifications 1n human blood using mass-spectrometric methods].

Transthyretin, one of the major plasma proteins, has a number of posttranslational modifications and mutations, some of which are associated with the development of severe diseases, for instance, familial amyloid neuropathy and Alzheimer's disease. In order to investigate the role of modified forms in the development of these diseases a complex analytical platform, based on two mass-spectrometric approaches (bottom-up and op-down) has been developed. The high efficiency of this method was shown using 10 plasma samples obtained from patients with Alzheimer's disease and healthy individuals.

Changes of protein profile of human urine after long-term orbital flights.

We analyzed protein profile of urine samples obtained from 7 Russian cosmonauts (age 35-51 years), participants of space flights on the International Space Station lasting for 169-199 days. Gradient chromatography with linear increase of eluent proportion was carried out in a system consisting of an Agilent 1100 chromatograph (Agilent Technologies Inc.) and a hybrid mass-spectrometer LTQ-FT Ultra (Thermo). The obtained results help to understand changes in the human body induced by space flight factors.

[Detection of renal and urinary tract proteins in the urine before and after space flight].

The urine protein composition (proteome) of healthy human was analyzed using proteomic techniques to obtain data in physiological condition and after six months space flights. It was shown that after long duration space flights in cosmonaut's urine reveals specific minor proteins which can be identified as proteins came from kidney and urinary tract.

[The study of cognitive functions and the brain electrical activity in wakefulness and night sleep in patients with lobe tumors]. / Izuchenie kognitivnykh funktsii i organizatsii bioelektricheskoi aktivnosti mozga v bodrstvovanii i vo vremya sna u patsientov s opukholyami lobnoi doli.

OBJECTIVE: To study cognitive dysfunction and brain electrical activity in sleep-wakefulness cycle in patients with frontal lobe tumors. MATERIAL AND METHODS: Twenty patients, aged 48.6±4.2 years, and ten healthy volunteers participated in the study. The first group included patients without cognitive impairment and tumors 8.9±5.1 cm3, the second group included patients with cognitive impairment and tumors 40.7±2.1 cm3. The battery of cognitive impairment tests was used. The EEG of wakefulness and night sleep was recorded. RESULTS: Cognitive impairment in patients with lobe tumors is associated with increases in delta/theta, and areactivity of the cortex in wakefulness, increases in delta/theta/alpha in REM and declining number of arousals in REM. CONCLUSION: The results of the study may be useful in early detection of biomarkers of the cognitive impairment in patients with frontal lobe tumors in order to increase the efficiency of rehabilitation of patients.

[Data filtration for more robust alignment of chromatograms of complex peptide mixtures].

In carrying out proteomic researches using mass-spectrometry there often arises a need to compare experimental data with each other (e.g. control of pathology, the labeled to unlabelled samples). If for peptide identification in different experiments one uses only their exact mass measurements and the retention time in the chromatographic column, difficulties with the identification of chromatographic peaks belonging to the same substances in different chromatograms come up (retention time normalization). Due to inevitable discrepancies in chromatographic conditions of experiments (replacement of chromatographic columns, small changes in mobile phase flow rate or solvent concentration) retention times of the same peptides will diverge from experiment to experiment. In this paper we offer a reliable method for selecting peaks from mass-chromatograms corresponding to the same peptides, which can later be used for retention time normalization (either linear or any other monotone function).

Light stress photodynamics of chlorophyll-binding proteins in Arabidopsis thaliana thylakoid membranes revealed by high-resolution mass spectrometric studies.

In higher plants the light energy is captured by the photosynthetic pigments that are bound to photosystem I and II and their light-harvesting complex (LHC) subunits. In this study, we examined the photodynamic changes within chlorophyll-protein complexes in the thylakoid membrane of Arabidopsis thaliana leaves adapted to low light and subsequently exposed to light stress. Chlorophyll-protein complexes were isolated using sucrose density gradient centrifugation and blue-native polyacrylamid gel electrophoresis (BN-PAGE). Proteome analysis was performed using SDS-PAGE, HPLC and high resolution mass spectrometry. We identified several rarely expressed and stress-induced chlorophyll-binding proteins, showed changes in localization of early light-induced protein family and LHC protein family members between different photosynthetic complexes and assembled/disassembled subcomplexes under light stress conditions and discuss their role in a variety of light stress-related processes.