{"title":"[The bioinformatic identification of proteins with varying levels of post-translational modifications in experimental ischemic stroke in mice].","authors":"V S Skvortsov, Ya O Ivanova, A I Voronina","doi":"10.18097/PBMC20216706475","DOIUrl":null,"url":null,"abstract":"<p><p>The experimental data obtained by Simats A. et al. (Molecular and Cellular Proteomics, 2020, 19(12), 1921-1936) was analysed using a bioinformatic approach. Original experimental results available in the ProteomeXchange database were obtained using a comprehensive multidomain approach to identify potential blood biomarkers in ischemic stroke in mice. The identification of peptides with post-translational modification (PTM) was performed by us using the raw data (accession code PXD016538). Only phosphorylation and deamination were considered as PTMs. Different combinations of data sets (ischemic tissue with intact tissue, ischemic tissue with control taken from mice after sham surgery, etc.) were compared both in terms of the ratio of abundance for the modified peptide to the unmodified variant and in terms of absolute values of abundance. The most likely change in precisely PTM levels was shown for 27 proteins, which include dynamin, glycogen phosphorylase and 70 kDa heat shock protein.</p>","PeriodicalId":8889,"journal":{"name":"Biomeditsinskaya khimiya","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biomeditsinskaya khimiya","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.18097/PBMC20216706475","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 0
Abstract
The experimental data obtained by Simats A. et al. (Molecular and Cellular Proteomics, 2020, 19(12), 1921-1936) was analysed using a bioinformatic approach. Original experimental results available in the ProteomeXchange database were obtained using a comprehensive multidomain approach to identify potential blood biomarkers in ischemic stroke in mice. The identification of peptides with post-translational modification (PTM) was performed by us using the raw data (accession code PXD016538). Only phosphorylation and deamination were considered as PTMs. Different combinations of data sets (ischemic tissue with intact tissue, ischemic tissue with control taken from mice after sham surgery, etc.) were compared both in terms of the ratio of abundance for the modified peptide to the unmodified variant and in terms of absolute values of abundance. The most likely change in precisely PTM levels was shown for 27 proteins, which include dynamin, glycogen phosphorylase and 70 kDa heat shock protein.
Simats a . et al. (Molecular and Cellular Proteomics, 2020, 19(12), 1921-1936)获得的实验数据使用生物信息学方法进行了分析。ProteomeXchange数据库中可用的原始实验结果是使用综合多域方法获得的,用于识别小鼠缺血性中风中潜在的血液生物标志物。我们使用原始数据(登录码PXD016538)进行翻译后修饰肽的鉴定。只有磷酸化和脱氨作用被认为是PTMs。不同的数据集组合(缺血组织与完整组织、缺血组织与假手术后小鼠的对照等)在修饰肽与未修饰变体的丰度比率以及丰度绝对值方面进行了比较。27种蛋白质的PTM水平最可能发生精确的变化,包括动力蛋白、糖原磷酸化酶和70 kDa热休克蛋白。
Biomeditsinskaya khimiyaBiochemistry, Genetics and Molecular Biology-Biochemistry, Genetics and Molecular Biology (all)
CiteScore
1.30
自引率
0.00%
发文量
49
期刊介绍:
The aim of the Russian-language journal "Biomeditsinskaya Khimiya" (Biomedical Chemistry) is to introduce the latest results obtained by scientists from Russia and other Republics of the Former Soviet Union. The Journal will cover all major areas of Biomedical chemistry, including neurochemistry, clinical chemistry, molecular biology of pathological processes, gene therapy, development of new drugs and their biochemical pharmacology, introduction and advertisement of new (biochemical) methods into experimental and clinical medicine etc. The Journal also publish review articles. All issues of journal usually contain invited reviews. Papers written in Russian contain abstract (in English).