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. Author manuscript; available in PMC: 2014 Dec 6.
Published in final edited form as: J Proteome Res. 2013 Oct 11;12(12):10.1021/pr400705q. doi: 10.1021/pr400705q

Figure 4. The PFM level information increases the number of protein identifications.

Figure 4

In (A) we display the number of proteins as a function of the PSM-derived q values (dashed line), and combined PFM+PSM-derived q value (solid line) for the yeast-01 dataset. In (B) and (C) we show the overlap between the yeast proteins identified at q < 0.01 when using the in silico AMT workflow, and when using only the PSMs, respectively.