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Background: Acute Myocardial Infarction (AMI) is a life-threatening cardiovascular disease involving disruption of blood flow to the heart, consequent tissue damage, and sometimes death. Peptidomics, an emerging branch of proteomics, has attracted wide attention. Methods: A comparative peptidomic profiling was used to explore changes induced by acute ischemic-hypoxia in primary cultured neonatal rat myocardial cells. Analysis of six-plex tandem mass tag (TMT) labelled peptides was performed using nanoflow liquid chromatography coupled online with an LTQ-Orbitrap Velos mass spectrometer. Results: A total of 220 differentially expressed peptides originating from 119 proteins were identified, of which 37 were upregulated and 183 were downregulated in cardiomyocytes exposed to hypoxia/ischemia conditions. Many of the identified peptides were derived from functional domains of proteins closely associated with cardiomyocyte structure or AMI. Conclusion: Numerous peptides may be involved in process of AMI. These results pave the way for future functional studies of the identified peptides.