Fig. 4.

Effects of the picked approach on focused data sets. A, To investigate the effect of the picked approach on studies of varying size, we plotted the increase of confidently identified proteins using the picked approach versus the number of proteins reported by the classic approach for 76 data sets (green dots). The picked approach invariably identifies more proteins than the classic approach and the difference increases with the number of proteins identified in a given data set. B, Reassessment of the number of proteins reported in a number of publications showed that the picked approach (blue) identified more proteins than the classic approach (red). It is also evident that the picked TDS is more conservative than the number of proteins reported in many of these publications (gray).