Feature selection algorithm for spray-from-tissue mass spectrometry

Sorokin, Anatoly; Zhvansky, Evgeny; Shurkhay, Vsevolod; Bocharov, K. V.; Popov, Igor; Levin, Nikita; Zubtsov, D. A.; Bormotov, Denis S.; Kostyukevich, Yury; Потапов, А А; Nikolaev, Eugene

doi:10.1177/1469066717721843

Cited by 7 publications

(7 citation statements)

References 24 publications

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“…Таким образом, для практического применения методов прямой масс-спектрометрии и прямой экстракции липидов из тканей требуется разработка специальных алгоритмов для анализа спектров. Этой же группой авторов [17] предложен алгоритм, предназначенный для анализа данных прямой масс-спектрометрии для определения физических границ опухолевой ткани.…”

Section: современные возможности масс-спектрометрии в нейроонкологииunclassified

“…Первые работы, в которых описаны исследования тканей методами прямой масс-спектрометрии, были выполнены с использованием метода десорбционно-электроспрейной ионизации (DESI), в котором микроэкстракция исследуемых молекул из образца с их последующей ионизацией осуществляется при взаимодействии заряженных капель водно-метанольной смеси с исследуемым образцом. Это позволяет получить данные о липидном профиле опухолевой ткани, а также распределении в ткани различных характерных водорастворимых онкометаболитов [15][16][17]. Основными молекулярными маркерами липидной природы, на основе которых проводится идентификация тканей при помощи описанных выше методов, являются насыщенные и ненасыщенные жирные кислоты (ЖК), глицерофосфоинозитолы, глицерофосфосерины, плазминил-глицерофосфоэтаноламины и сульфатиды.…”

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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

Никитин¹,

Потапов²,

Ryzhova³

et al. 2018

Vopr. neirokhir.

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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.

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Section: современные возможности масс-спектрометрии в нейроонкологииunclassified

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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

Никитин¹,

Потапов²,

Ryzhova³

et al. 2018

Vopr. neirokhir.

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“…Ambient MS profiles of brain tumor tissues are complex data due to the variety of lipids and metabolites extracted during analysis. However, further statistical analysis and machine learning algorithms allow us to remove the matrix effect and extract features for further tissue differentiation 36 . PCA (Fig.…”

Section: Resultsmentioning

confidence: 99%

Inline cartridge extraction for rapid brain tumor tissue identification by molecular profiling

Pekov

Eliferov

Sorokin

et al. 2019

Sci Rep

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The development of perspective diagnostic techniques in medicine requires efficient high-throughput biological sample analysis methods. Here, we present an inline cartridge extraction that facilitates the screening rate of mass spectrometry shotgun lipidomic analysis of tissue samples. We illustrate the method by its application to tumor tissue identification in neurosurgery. In perspective, this high-performance method provides new possibilities for the investigation of cancer pathogenesis and metabolic disorders.

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“…The molecular profile analysis is challenged by the complexity of data, the matrix effect, and possible signal instability. To overcome such complications, it is usually suggested to implement special algorithms for data evaluation, preprocessing, and further analysis using machine learning [21][22][23][24][25][26][27][28].…”

Section: Discussionmentioning

confidence: 99%

Lipid Profiles of Human Brain Tumors Obtained by High-Resolution Negative Mode Ambient Mass Spectrometry

Zavorotnyuk

Pekov

Sorokin

et al. 2021

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Alterations in cell metabolism, including changes in lipid composition occurring during malignancy, are well characterized for various tumor types. However, a significant part of studies that deal with brain tumors have been performed using cell cultures and animal models. Here, we present a dataset of 124 high-resolution negative ionization mode lipid profiles of human brain tumors resected during neurosurgery. The dataset is supplemented with 38 non-tumor pathological brain tissue samples resected during elective surgery. The change in lipid composition alterations of brain tumors enables the possibility of discriminating between malignant and healthy tissues with the implementation of ambient mass spectrometry. On the other hand, the collection of clinical samples allows the comparison of the metabolism alteration patterns in animal models or in vitro models with natural tumor samples ex vivo. The presented dataset is intended to be a data sample for bioinformaticians to test various data analysis techniques with ambient mass spectrometry profiles, or to be a source of clinically relevant data for lipidomic research in oncology.

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Feature selection algorithm for spray-from-tissue mass spectrometry

Cited by 7 publications

References 24 publications

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

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

Inline cartridge extraction for rapid brain tumor tissue identification by molecular profiling

Lipid Profiles of Human Brain Tumors Obtained by High-Resolution Negative Mode Ambient Mass Spectrometry

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