Identification of Peptides Encoded by Small Open Reading Frames in Microalgae by Mass Spectrometry

SEPs are important as co-operators of various biological processes with canonical proteins. In microalgae, they are reported to be involved in photosynthesis, nitrogen metabolism, stress response, and so on. Because of low abundance and small molecular weight, identifying SEPs in proteomics is usually challenging, requiring specially designed technical strategies for sample handling and data analysis. Here, we present two method examples for SEP in microalgae (one cyanobacterium and one green alga), from SEP extraction and enrichment to database search, aiming to achieve an ideal identification of SEPs while reducing the interference of canonical proteins. This chapter will provide a reference procedure for SEP exploration in microalgae.