The differentially expressed proteins of mutated C. pyrenoidosa obtained by N+ ion implantation were isolated and identified using proteomics analysis method combining the isobaric tags for relative and absolute quantitation and liquid chromatography-tandem mass spectrometry techniques. The functions of these proteins were also investigated toward elucidating the fundamental mechanism by which ion implantation promotes the growth of C. pyrenoidosa and accumulation of lipids at the molecular level. In total, 17 differentially expressed proteins were identified in algae cells, including 3 up-regulated and 14 down-regulated proteins. Combining these results with the central carbon metabolism network of C. pyrenoidosa cells and the lipid metabolism pathway showed that N+ ion implantation can promote the synthesis of chlorophyll by up-regulating magnesium protoporphyrin IX methyltransferase to further improve the carbon sequestration efficiency of algae cells. These phenomena result in a greater production rate of organic material and therefore increased biomass. In addition, N+ ion implantation can enhance the glycolysis and pentose phosphate pathways by down-regulating fructose-bisphosphate aldolase and transketolase. These effects ultimately promote the accumulation of lipids by C. pyrenoidosa. These findings provide a rationalization of the mechanism by which ion implantation-induced mutagenesis promoting high lipid productivity in C. pyrenoidosa CVM at the proteomics level. (c) 2020 Elsevier Ltd. All rights reserved.