Figure 1

Reproducibility of protein identification between individual mice. A. Renal cortical proteins isolated from three mice, were extracted, digested with trypsin, separated by SCX into 60 fractions, and for each mouse, 14 consecutive SCX fractions with retention times between 20 and 34 min were selected for LC-MS/MS analysis. B. The NSAF values of the proteins identified as common in all three mice. ■, NSAF values of the proteins identified from mouse A; ▲, NSAF values of the proteins identified from mouse B; ◆, NSAF values of the proteins identified from mouse C; and ●, the mean of the NSAF values. C. The NSAF values of the proteins identified from all of the three mice. ◇, the mean of the NSAF values of the proteins identified as common in all three mice; ■, the mean of the NSAF values of the proteins identified in two out of three mice; △, the NSAF values of the protein identified in only one mouse. D. To examine reproducibility of the 2D-LC-MS/MS method, we analyzed one SCX fraction by LC-MS/MS three times. E. The NSAF values of the proteins identified from all of the three LC-MS/MS runs. ◆, the mean of the NSAF values of the proteins identified as common in all three LC-MS/MS runs; ×, the mean of the NSAF values of the proteins identified in two out of three LC-MS/MS runs; and △, the NSAF values of the protein identified in only one LC-MS/MS run.