Abstract
A comparative protein profile analysis of 17 blood plasma samples from patients with ischemia and 20 samples from healthy volunteers was carried out using ultra-high resolution mass spectrometry. The analysis of measurements was performed using the proteomics search engine OMSSA. Normalized spectrum abundance factor (NSAF) in the biological samples was assessed using SearchGUI. The findings of mass spectrometry analysis of the protein composition of blood plasma samples demonstrate that the depleted samples are quite similar in protein composition and relative abundance of proteins. By comparing them with the control samples, we have found a small group of 44 proteins characteristic of the blood plasma samples from patients with chronic cerebral ischemia. These proteins contribute to the processes of homeostasis maintenance, including innate immune response unfolding, the response of a body to stress, and contribution to the blood clotting cascade.
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NSAF, normalized spectral abundance factor, DOI: https://doi.org/10.1002/rcm.7829
References
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32(90001):D115–D119. https://doi.org/10.1093/nar/gkh131
Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L (2011) Compomics-utilities: an open-source java library for computational proteomics. BMC Bioinformatics 12(1):70. https://doi.org/10.1186/1471-2105-12-70
Bokeriya LA, Stupakov IN, Gudkova RG (2012) Successes and problems of Russian cardiosurgery. Zdravookhranenie 3:24–33
Bubis JA, Levitsky LI, Ivanov MV, Tarasova IA, Gorshkov MV (2017) Comparative evaluation of label-free quantification methods for shotgun proteomics. Rapid Commun Mass Spectrom 31(7):606–612. https://doi.org/10.1002/rcm.7829
Dong L, Hou R, Xu Y, Yuan J, Li L, Zheng C, Zhao H (2015) Analyzing the correlation between the level of serum markers and ischemic cerebral vascular disease by multiple parameters. Comput Math Methods Med 2015:972851. https://doi.org/10.1155/2015/972851
Elias JE, Gygi SP (2010) Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol 604:55–71. https://doi.org/10.1007/978-1-60761-444-9_5
Famakin BM (2014) The immune response to acute focal cerebral ischemia and associated post-stroke immunodepression: a focused review. Aging Dis 5(5):307–326. https://doi.org/10.14336/AD.2014.0500307
Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH (2004) Open mass spectrometry search algorithm. J Proteome Res 3(5):958–664. https://doi.org/10.1021/pr0499491
Kaysheva AL, Kopylov AT, Yurov IY, Archakov AI, Ivanov YD (2016) Proteomic analysis of blood serum protein profiles in children with autism. Voprosy Prakticheskoi Pediatrii 11(5):12–17. https://doi.org/10.20953/1817-7646-2016-5-12-17
Kaysheva AL, Kopylov AT, Pleshakova TO, Iourov IY, Vorsanova SG, Yurov YB, Shchetkin AA, Archakov AI, Ivanov YD (2017) Proteomic analysis of serum proteins of children with autism. Biotecnol Apl 34(1):2211–2214
Martynchik SA, Sokolova OV (2013) Medical and economic assessment and rationale for improving organization of inpatient care for cerebral stroke. Social aspects of population health 30(2).
Petrak J, Ivanek R, Toman O, Cmejla R, Cmejlova J, Vyoral D, Zivny J, Vulpe CD (2008) Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins. Proteomics 8(9):1744–1749. https://doi.org/10.1002/pmic.200700919
Powell DW, Weaver CM, Jennings JL, McAfee KJ, He Y, Weil PA, Link AJ (2004) Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol 24(16):7249–7259. https://doi.org/10.1128/MCB.24.16.7249-7259.2004
Suslina ZA, Varakin YY, Vereshchagin NV (2009) Clinic and epidemiological researches as a perspective direction of cerebral pathology study (the first report). Annaly nevrologii 3:4–11
Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L (2011) SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 11(5):996–999. https://doi.org/10.1002/pmic.201000595
Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L, Barsnes H (2015) PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol 33(1):22–24. https://doi.org/10.1038/nbt.3109
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The study was carried out in the framework of the Program of Fundamental Research of State Academies of Sciences for 2013-2020.
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Kaysheva, A.L., Kopylov, A.T., Ponomarenko, E.A. et al. Relative Abundance of Proteins in Blood Plasma Samples from Patients with Chronic Cerebral Ischemia. J Mol Neurosci 64, 440–448 (2018). https://doi.org/10.1007/s12031-018-1040-3
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DOI: https://doi.org/10.1007/s12031-018-1040-3