Primenenie metodov pryamoj mass-spektrometrii yavlyaetsya odnim iz perspektivnyh podhodov k uluchsheniyu polnoty rezekcii glial'nyh opuholej za schet ispol'zovaniya dopolnitel'nogo sposoba povysheniya tochnosti opredeleniya granic opuholi neposredstvenno v hode nejrohirurgicheskogo vmeshatel'stva. Massivy dannyh, nakaplivaemye v hode aprobacii podobnyh tekhnologij, mogut byt' ispol'zovany i dlya provedeniya fundamental'nyh issledovanij s cel'yu vyyavleniya metabolicheskih izmenenij, soprovozhdayushchih rost opuholi. Cel'yu raboty bylo provesti analiz izmenenij v lipidnom sostave kletochnyh membran diffuznyh i anaplasticheskih astrocitom na osnove dannyh, sobrannyh v hode pryamogo mass-spektrometricheskogo profilirovaniya tkanej, issechennyh v hode planovogo nejrohirurgicheskogo vmeshatel'stva. Lipidnye profili, poluchennye v hode issledovaniya obrazcov opuholevyh tkanej (n = 43) metodom protochnoj mikroekstrakcii v kartridzhe, analizirovali s ispol'zovaniem linejnogo diskriminantnogo analiza so szhatiem, chto pozvolilo vydelit' nabor lipidov, soderzhanie kotoryh izmenyaetsya pri uvelichenii stepeni zlokachestvennosti opuholi. Raznoobrazie lipidov snizhaetsya po mere povysheniya stepeni zlokachestvennosti, tak, soderzhanie 13 fosfolipidov, prinadlezhashchih k 6 razlichnym podklassam, okazyvaetsya snizhennym v anaplasticheskih opuholyah po sravneniyu s diffuznymi. S rostom zlokachestvennosti opuholi umen'shayutsya kak srednij razmer zhirnokislotnyh ostatkov polyarnyh lipidov, tak i stepen' ih nenasyshchennosti. Poluchennye rezul'taty horosho soglasuyutsya s dannymi, poluchennymi ranee v ramkah issledovaniya vysokozlokachestvennyh glial'nyh opuholej, i podtverzhdayut biohimicheskie predstavleniya o pereprogrammirovanii metabolizma v hode malignizacii nejroglii.

Radikal'noe udalenie opuholi do sih por ostaetsya naibolee effektivnym metodom lecheniya onkologicheskih zabolevanij golovnogo mozga. Zadachi intraoperacionnogo monitoringa na segodnyashnij den' reshayut s pomoshch'yu pozitronno-emissionnoj tomografii, magnitno-rezonansnoj tomografii i gistohimicheskogo analiza, odnako oni trebuyut primeneniya dorogostoyashchego oborudovaniya vysokokvalificirovannym personalom, poetomu do sih por ne poluchili shirokogo rasprostraneniya. V kachestve al'ternativy vozmozhno primenenie metodov mass-spektrometrii bez probopodgotovki s posleduyushchim analizom mass-spektrometricheskih dannyh metodami mashinnogo obucheniya. Tak kak dlya mass-spektrometrii bez probopodgotovki harakterny bolee bogatye i raznoobraznye po kolichestvu pikov spektry, ee primenenie trebuet special'noj predvaritel'noj obrabotki eksperimental'nyh dannyh. Cel'yu issledovaniya bylo razrabotat' metody opredeleniya optimal'nyh znachenij parametrov predvaritel'noj obrabotki dannyh mass-spektrometrii bez probopodgotovki. V rabote predstavleny dva takih metoda, a takzhe privedeny konkretnye znacheniya parametrov dlya dannyh, poluchennyh s pomoshch'yu mass-spektrometra Thermo LTQ XL Orbitrap ETD.

Radical tumor resection is still the most effective treatment method for brain tumors. The problems of intraoperative monitoring are currently solved using positron emission tomography, magnetic resonance imaging, and histochemical analysis, however, these require using expensive equipment by highly qualified personnel and are therefore still not widely available. As an alternative, it is possible to use mass spectrometry methods without sample preparation and then the analysis of mass spectrometry data involving the use of machine learning methods. The spectra that are more rich and diverse in terms of peak number are typical for mass spectrometry without sample preparation, therefore the use of this method requires specific pre-processing of experimental data. The study was aimed to develop the methods to determine the optimal parameter values for pre-processing of the data acquired by ambient ionization mass spectrometry. The paper presents two such methods and provides specific parameter values for the data acquired using the Thermo LTQ XL Orbitrap ETD mass spectrometer.

The use of ambient ionization mass spectrometry methods is one of the promising approaches to the impovement of glial tumor resection completeness by using an additional method to improve the tumor margin identification accuracy during the neurosurgical intervention itself. The amounts of data accumulated when testing such techniques can be also used in fundamental research to identify metabolic alterations associated with the tumor growth. The study was aimed to assess changes in the cell membrane lipid composition of diffuse and anaplastic astrocytomas based on the data acquired by ambient ionization mass spectrometry profiling of the tissues excised during the elective neurosurgical intervention. The lipid profiles obtained when assessing the tumor tissue samples (n = 43) by flow microextraction in a cartridge were subjected to shrinkage linear discriminant analysis enabling extraction of a number of lipids, the levels of which changed with increasing tumor grade. The lipid diversity decreased with increasing grade. Thus, the levels of 13 phospholipids belonging to six different subclasses turned out to be decreased in anaplastic tumors compared to diffuse ones. Both average size of the polar lipid fatty acid residues and their degree of unsaturation decrease with increasing tumor grade. The findings agree well with the data of the earlier study of high-grade glial tumors and confirm the biochemical view of metabolic reprogramming associated with malignant transformation of neuroglia.

The primary method of initial treatment of meningiomas is radical neurosurgical intervention. Various methods of intraoperative diagnostics currently in development aim to improve resection efficiency; we focus on methods based on molecular profiling using ambient ionization mass spectrometry. Such methods have been proven effective on various tumors, but the specifics of the molecular structure and the mechanical properties of meningiomas raise the question of applicability of protocols developed for other conditions for this particular task. The study aimed to compare the potential clinical use of three methods of ambient ionization in meningioma sample analysis: spray from tissue, inline cartridge extraction, and touch spherical sampler probe spray. To this end, lipid and metabolic profiles of meningioma tissues removed in the course of planned neurosurgical intervention have been analyzed. It is shown that in clinical practice, the lipid components of the molecular profile are best analyzed using the inline cartridge extraction method, distinguished by its ease of implementation and highest informational value. Analysis of oncometabolites with low molecular mass is optimally performed with the touch spherical sampler probe spray method, which scores high in both sensitivity and mass-spectrometric complex productivity.

Osnovnoy metod lecheniya meningiom na pervom etape yavlyayetsya neyrokhirurgicheskim vmeshatel'stvom s ostorozhnost'yu. Dlya rassmotreniya polnoty rezektsii v nastoyashcheye vremya razrabatyvayutsya razlichnyye podkhody k intraoperatsionnoy diagnostike, v chastnosti, opirayushchiyesya na printsipy molekulyarnogo profilirovaniya. Ustanovlennyye na mass-spektrometrii s pryamoy ionizatsiyey, takiye metody realizuyut svoyu effektivnost' na razlichnykh vidakh opukholey, odnako osobennosti molekulyarnoy struktury i mekhanicheskiye kharakteristiki meningiom ne pozvolyayut effektivno translirovat' protokoly, razrabotannyye dlya drugikh nozologiy. Tsel'yu raboty bylo primeneniye sravneniya vozmozhnostey trekh metodov pryamoy ionizatsii dlya issledovaniy obraztsov meningiom: metod pryamogo spreya tkani, metod kartridzhnoy ekstraktsii i metod ionizatsii s poverkhnosti sfericheskogo probootbornika. Dlya etogo analizirovali lipidnyy i metabolicheskiy profil' tkaney s meningiom, issechennykh v khode planovogo neyrokhirurgicheskogo vmeshatel'stva. Bylo prodemonstrirovano, chto dlya analiza primeneniya lipidnykh molekul molekulyarnogo profilya optimal'nym dlya klinicheskogo primeneniya yavlyayetsya metod kartridzhnoy ekstraktsii, otlichayushchiysya naiboleye prostoy realizatsiyey i vysokoy informativnost'yu. Dlya analiza onkometabolov s maloy molekulyarnoy massoy yavlyayetsya luchshim vyborom metoda ionizatsii poverkhnosti sfericheskogo probootbornika, dostizheniyem vysokoy chuvstvitel'nosti i nailuchshey proizvoditel'nost'yu mass-spektrometricheskogo kompleksa.

The analysis of data obtained using ambient mass spectrometric profiling of clinical samples of primary and secondary human glioblastomas ex vivo, revealed changes in the lipid composition of tissues accompanying the development of grade IV glial tumors (according to the WHO classification). It has been shown that both primary and secondary (developed from astrocytoma) tumors are enriched with mono- and di-unsaturated phosphatidylcholines (PC 26:1, 30:2, 32:1, 32:2, 34:1, 34:2). At the same time, the content of saturated and polyunsaturated phosphatidylcholines and phosphatidylethanolamines decreases. These changes are associated both with altered availability of polyunsaturated fatty acids and activation of de novo synthesis and beta-oxidation of fatty acids under conditions of oxygen starvation in the tumor body.

Background: The development of direct ambient ionization methods makes way for fast mass-spectrometry profiling of biological samples, which has great potential in medicine. Those methods, unlike traditional mass spectrometric analysis with chromatographic separation, are not able to take into account inter-ion interaction, ion suppression, and matrix effect due to the absence of chromatographic separation of the mixture components. So dynamics of ion current during direct ambient ionization mass-spectra is governed by the component micro-extraction and electrospray ionization influenced by the geometry of the sample, its position, and internal heterogeneity. Despite the progress in mass-spectrometry of biological samples, not much is known about the influence of sample type and structure on its molecular profile peculiarities. Methods: In this work, we propose to use analysis of the correlation between individual ion currents for a better understanding of ion current variability sources and grouping ions of high biological importance. Several fragments of glioblastoma tissue from a single patient are used for these purposes. Results: Ion currents have different dynamics considering different ions in different fragments. The correlation of two selected ion currents could be positive or negative for single fragment measurement. Correlations have persistent or alternating signs in different fragments for two selected ions. The spread of correlations of each pair of ion currents is calculated for evaluation of the signs’ stability. Conclusions: We were able to group ions according to the primary reason for their variabilities such as micro-extraction, mass-spectrometry measurement, or specimens' properties. Such grouping would allow the development of more reliable and reproducible methods of mass-spectrometry data analysis and improve the accuracy of results of its application in medicine.

SUMMARY Mass spectrometry methods are widely used for the analysis of biological and medical samples. Recently developed methods such as DESI, REIMS, 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 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 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.

Express MS identification of biological tissues has become a much more accessible research method due to the application of direct specimen ionization at atmospheric pressure. In contrast to traditional methods of analysis employing GC-MS methods for determining the molecular composition of the analyzed objects it eliminates the influence of mutual ion suppression. Despite significant progress in the field of direct MS of biological tissues, the question of mass spectrometric profile attribution to a certain type of tissue still remains open. The use of modern machine learning methods and protocols (e.g., "random forests") enables us to trace possible relationships between the components of the sample MS profile and the result of brain tumor tissue classification (astrocytoma or glioblastoma). In this study it has been shown that the most pronounced differences in the mass spectrometric profiles of these tumors are due to their lipid composition. Detection of statistically significant differences in lipid profiles of astrocytoma and glioblastoma may be used to perform an express analysis during surgery and inform the neurosurgeon what type of malignant tissue he is working with. The ability of accurate determination of the tumor boundaries significantly improves the quality of surgical intervention and postoperative rehabilitation, as well as the duration and quality of life of patients.

The paper presents a method for rapid multi-omics investigation of biological samples using polypropylene bulk porous samplers. The use of porous samplers makes it easy to collect samples from the surface of the skin, mucous membranes, and biological fluids even in a field, and the surfaces of wounds and injuries. Collected samples do not require special storage conditions, and the samplers are lightweight and very compact. They can be used to monitor the condition of cosmonauts before, during, and after the spaceflight with the same sample collection method. The analysis of biomaterial applied to the sampler is performed using direct mass spectrometry methods, similar to the dried blood spot technique that is already used in clinical practice. However, bulk porous samplers allow expanding the range of analytes ionization conditions, which increases the stability and reliability of the ionization process, which expands the variety of analyzed molecules. The proposed method can be used to study compounds of various classes, including proteins, lipids, and metabolites, to systematically monitor the status of people in extreme conditions (athletes, astronauts), or to study the condition of patients in the clinic.