Figure 2

Mass spectrometry analysis of TAP tag elutions. Calmodulin elutions from RpoC-TAP or RNase R-TAP purifications were analyzed using mass spectrometry. Row data were subsequently treated by MaxQuant software for label free quantification of proteins amount in the sample (expressed as intensity value). In blue are represented the group of proteins that were detected with higher scores. (A) Proteins identified in RpoC-TAP sample. Intensity values of all proteins identified in calmodulin elution (x-axis) were plotted with specificity value of each protein (y-axis). Specificity is expressed as protein intensity value in the sample divided by intensity of given protein in the control sample. RNase R-TAP was the control sample for RpoC-TAP purification. (B) Proteins identified in RNase R-TAP sample. Intensity values of all proteins identified in calmodulin elution (x-axis) were plotted with specificity value of each protein (y-axis). RpoC-TAP was considered as control sample for RNase R-TAP purification. (C) Changes of protein content of RNase R-TAP elution sample in response to RNase A treatment. Intensity values of proteins detected in RNase R-TAP elution (RNRTAP) were plotted against intensities of proteins detected in RNase R-TAP sample from the experiment where RNase A was included into purification steps (RNRTAP + RNase A). Points with intensity values over threshold of 10⁹ are highlighted. (D) Changes of protein content of RNase R-TAP elution samples collected from exponentially growing cells compared to cells after cold shock (RNRTAP). Intensities of proteins detected in samples collected from the cells grown in different conditions were plotted. Points with intensity values over threshold of 10⁹ are highlighted.