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Background   Ophiocordyceps sinensis  is an important traditional Chinese medicine for its comprehensive active ingredients, such as cordycepin, cordycepic acid, and  Cordyceps  polysaccharide.  O. sinensis  zjut ,  a special strain isolated from  O. sinensis,  has similar pharmacological functions to wild  O. sinensis . Currently,  O. sinensis  with artificial cultivation has been widely studied, but systematic fundamental research at protein levels has not been determined.    Results  Proteomes of  O. sinensis  zjut at different culture periods (growth period, 3rd day; pre-stable period, 6th day; and stable period, 9th day) were relatively quantified by relative isotope markers and absolute quantitative technology. In total, 4005 proteins were obtained and further annotated with Gene Ontology, Kyoto Encyclopedia of Genes and Genomes database. Based on the result of the annotations, metabolic pathways of active ingredients, amino acids and fatty acid were constructed, and the related enzymes were exhibited. Subsequently, comparative proteomics of  O. sinensis  zjut identified the differentially expressed proteins (DEPs) by growth in different culture periods, to find the important proteins involved in metabolic pathways of active ingredients. 605 DEPs between 6d-VS-3d, 1188 DEPs between 9d-VS-3d, and 428 DEPs between 9d-VS-6d were obtained, respectively.    Conclusion  This work provided scientific basis to study protein profile and comparison of protein expression levels of  O. sinensis  zjut, and it will be helpful for metabolic engineering works to active ingredients for exploration, application and improvement of this fungus.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-020-07298-z.

Proteome sequencing and analysis of Ophiocordyceps sinensis at different culture periods