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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 3. The in silico AMT workflow.

Figure 3

Our approach includes two complementary workflows. The first one, depicted on the left-side, includes the typical steps of a shotgun experiment, where we employ the fragmentation spectra to derive protein probabilities. In a second workflow, we map the peptides that did not match a fragmentation spectrum to the MS1-features, and use the resultant peptide-feature matches to derive a new set of protein probabilities. Finally, we combine the two statistics to derive improved protein-level confidence measures.