Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia

Kaysheva, Anna L.; Kopylov, Arthur T.; Ponomarenko, Elena A.; Kiseleva, Olga I.; Teryaeva, N. B.; Потапов, А А; Izotov, Alexander; Morozov, Sergey G.; Kudryavtseva, Valeria Yu.; Archakov, Alexander I.

doi:10.1007/s12031-018-1040-3

Cited by 11 publications

(6 citation statements)

References 12 publications

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“…We followed the methods of A. L. Kaysheva et al 2019 [73]. Blood plasma at a volume of 40 µL was brought to a final volume of 500 µL by adding a solution of 0.1% deoxycholic acid sodium salt, 6% acetonitrile, and 75 mM triethylammonium bicarbonate, pH 8.5.…”

Section: Sample Preparation For Ms Analysismentioning

confidence: 99%

“…The protein solution was added to with modified (acetylated at primary amino groups of lysine) trypsin at an enzyme-to-substrate ratio of 1:50. After this, a second aliquot of trypsin was added at a ratio of 1:100 and incubated at 37 • C, which was continued for an additional 12 h [73]. The sample preparation protocol is presented in detail in the PRIDE Project PXD015163.…”

Section: Sample Preparation For Ms Analysismentioning

confidence: 99%

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Revelation of Proteomic Indicators for Colorectal Cancer in Initial Stages of Development

et al. 2020

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Background: Colorectal cancer (CRC) at a current clinical level is still hardly diagnosed, especially with regard to nascent tumors, which are typically asymptotic. Searching for reliable biomarkers of early diagnosis is an extremely essential task. Identification of specific post-translational modifications (PTM) may also significantly improve net benefits and tailor the process of CRC recognition. We examined depleted plasma samples obtained from 41 healthy volunteers and 28 patients with CRC at different stages to conduct comparative proteome-scaled analysis. The main goal of the study was to establish a constellation of protein markers in combination with their PTMs and semi-quantitative ratios that may support and realize the distinction of CRC until the disease has a poor clinical manifestation. Results: Proteomic analysis revealed 119 and 166 proteins for patients in stages I–II and III–IV, correspondingly. Plenty of proteins (44 proteins) reflected conditions of the immune response, lipid metabolism, and response to stress, but only a small portion of them were significant (p < 0.01) for distinguishing stages I–II of CRC. Among them, some cytokines (Clusterin (CLU), C4b-binding protein (C4BP), and CD59 glycoprotein (CD59), etc.) were the most prominent and the lectin pathway was specifically enhanced in patients with CRC. Significant alterations in Inter-alpha-trypsin inhibitor heavy chains (ITIH1, ITIH2, ITIH3, and ITIH4) levels were also observed due to their implication in tumor growth and the malignancy process. Other markers (Alpha-1-acid glycoprotein 2 (ORM2), Alpha-1B-glycoprotein (A1BG), Haptoglobin (HP), and Leucine-rich alpha-2-glycoprotein (LRG1), etc.) were found to create an ambiguous core involved in cancer development but also to exactly promote tumor progression in the early stages. Additionally, we identified post-translational modifications, which according to the literature are associated with the development of colorectal cancer, including kininogen 1 protein (T327-p), alpha-2-HS-glycoprotein (S138-p) and newly identified PTMs, i.e., vitamin D-binding protein (K75-ac and K370-ac) and plasma protease C1 inhibitor (Y294-p), which may also contribute and negatively impact on CRC progression. Conclusions: The contribution of cytokines and proteins of the extracellular matrix is the most significant factor in CRC development in the early stages. This can be concluded since tumor growth is tightly associated with chronic aseptic inflammation and concatenated malignancy related to loss of extracellular matrix stability. Due attention should be paid to Apolipoprotein E (APOE), Apolipoprotein C1 (APOC1), and Apolipoprotein B-100 (APOB) because of their impact on the malfunction of DNA repair and their capability to regulate mTOR and PI3K pathways. The contribution of the observed PTMs is still equivocal, but a significant decrease in the likelihood between modified and native proteins was not detected confidently.

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Section: Sample Preparation For Ms Analysismentioning

confidence: 99%

Section: Sample Preparation For Ms Analysismentioning

confidence: 99%

Revelation of Proteomic Indicators for Colorectal Cancer in Initial Stages of Development

et al. 2020

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“…Fragmentation was performed in the high-energy activation mode with rating 27% (per weight of m / z 400 and charge z = 2 + ) and variation per each scanning within ±15%. MS/MS spectra in a RAW format were processed in Mass Hunter version В 2.0 [3,4] Obtained data were deposited to the ProteomeXchange Consortium via the PRIDE [5] partner repository with the dataset identifiers PXD015164, PXD015164. Mass spectrometric measurements were performed using the equipment of “Human Proteome” Core Facility of the Institute of Biomedical Chemistry (Russia, Moscow).…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Proteome dataset of mouse macrophage cell line infected with tick-borne encephalitis virus

et al. 2020

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We report the proteomic datasets on the mouse macrophage cell line PMJ2R infected with tick-borne encephalitis virus (TBEV) for two and six days. Data were acquired using shotgun ultra-high resolution mass spectrometry. Peptide identifications were done using the Mascot version 2.4 (Matrix Science), and quantification was performed by a label-free approach. Protein profiles of early (two days) and late (six days) stages of infection were compared between each other and the respective control samples.Protein profiles of infected and control samples differed in the number of identified proteins and their relative abundances. Proteins detected in the TBEV-infected cells were involved in various processes related to the infection, including defense response against the virus, regulation of viral process, negative regulation of viral genome replication, RNA binding, or innate immune response. Also, proteins specific for the early and late stages of infection were identified.

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“…Isolation of precursory ions was performed with the width of w = ± 1 Th within the range from 9 to 17 s from the peak apex for the tandem scanning. HPLC-MS/MS spectra in the RAW format were processed in Mass Hunter version В 2.0 [7].…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Pilot data of serum proteins from children with autism spectrum disorders

et al. 2019

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Protein profiles of 13 serum samples from children with autism spectrum disorders (ASD) and 11 serum samples from healthy volunteers was obtained using panoramic ultra-high resolution mass spectrometry. The analysis of measurements was performed using the proteomics search engine. We identified a group of 74 proteins which we term a “protein fingerprint” specific for serum samples collected from children with autism. Components of the protein fingerprint are involved in hemostasis maintenance including biological regulation, the response to stimulus, regulation of metabolism, and proteins of the immune system.

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Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia

Cited by 11 publications

References 12 publications

Revelation of Proteomic Indicators for Colorectal Cancer in Initial Stages of Development

Revelation of Proteomic Indicators for Colorectal Cancer in Initial Stages of Development

Proteome dataset of mouse macrophage cell line infected with tick-borne encephalitis virus

Pilot data of serum proteins from children with autism spectrum disorders

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