The cell membrane fraction of Chlamydomonas cw15 and the ciliary membrane fraction of Chlamydomonas cc125 were extracted by aqueous two-phase extraction and sucrose density gradient centrifugation, respectively. The membrane fractions were dissolved in 8 M urea to obtain plasma membrane proteins (PM) and ciliary membrane proteins (FM). TMT labeling reagents (126-129) were used to label the two biological replicates of each fraction separately. The labeled peptides were fractionated into 10 fractions by liquid chromatography, followed by mass spectrometry analysis.