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Proteomics analysis of unsequenced organisms (orphan species) is rare. The mass spectrometry-based protein identification of these species results in matching with protein sequences of other species and lower identification scores. One such species is Prototheca zopfii, an achlorophyllous alga associated with therapy-resistant bovine mastitis and rare human infection. Two genotypes of Prototheca zopfii have been described: non-pathogenic genotype 1 and pathogenic genotype 2. Recently, proteomic differences between these two genotypes were investigated using 2D-DIGE MALDI-TOF MS analysis (1) and NCBI database resulted in identification of 110 out of 209 proteins spots. Despite 280 Prototheca proteins entries (P. wickerhamii -272, P. zopfii -2, P. blaschkeae-1 and deduced from microbes-3) in the database, the rate of identification was low (52%) and the matching occurred with proteins from Prototheca (4%), other algae (36%), bacteria (39%), plants (10%), fungi (4%), and others (7%). Expressed sequence tag (EST)-based protein identification might enhance identification rate due to the larger number of EST entries (5906) in the database.
1. Murugaiyan et al, 2013, Proteomics. 13, 2664-9