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. Author manuscript; available in PMC: 2018 Feb 3.
Published in final edited form as: J Proteome Res. 2016 Dec 2;16(2):609–618. doi: 10.1021/acs.jproteome.6b00698

Figure 3.

Figure 3

Efficiency of identification of new proteoforms from a single GELFrEE fraction using three technical replicates under Xcalibur data-dependent or AUTOPILOT data acquisition. The number of new proteoforms identified in each technical replicate for GELFrEE fractions 1, 2, and 3 is normalized over the total number of new proteoforms identified in the single GELFrEE fraction of interest. (A) The data-dependent top-2 method shows that for the three fractions considered, the first technical replicate provides the highest number of new proteoforms, and the capability of the data-dependent method of finding new confident proteoforms decreases with the number of technical replicates. (B) The AUTOPILOT experiments show that the SIM march with 50 m/z windows (2nd technical replicate) outperforms the standard AUTOPILOT acquisition based on the MS1–MS2 scheme (1st technical replicate) in two fractions out of three. Conversely, the SIM march composed by eight SIM events (3rd technical replicate) produces the lowest number of new identified proteoforms.