Comparison of the protein composition of cilia isolated from wild-type (WT) and CCDC113-KO cells using mass spectrometry.

About 0.2 mg of ciliary proteins was analyzed in WT and CCDC113-KO, sample 1, and about 0.1 mg of proteins in the case of CCDC113-KO, sample 2. Proteins present in both control and experimental samples are highlighted in green (exp1) or blue (exp2). In previously published cilia and flagella proteomes [32,79–81] the number of the identified proteins was e.g. 1134 proteins (482 identified by 1 peptide) in Chlamydomonas flagella [32] or 751 proteins in Trypanosoma flagella [81]. A higher number of the identified ciliary protein candidates in Tetrahymena ciliome could be due to: (i) differences in the cilia preparation method and analysis of whole cilia versus ciliary fractions, (ii) initial amount of ciliary proteins that were analyzed by mass spectrometry, (iii) presence of more than one ortholog of some ciliary proteins (e.g ciliary dyneins) in Tetrahymena; (iv) presence of ciliate-specific proteins as we determined by BlastP search using NCBI database. A similar number of putative ciliary proteins was obtained in our previous studies [41]. (XLSX)