Fig. 5

Transcriptome-informed post hoc filtering and reduced database search strategies similarly reduce protein identification ambiguity. A Illustration of the transcriptome-informed post hoc filtering strategy. First, an MS/MS search was performed against the full canonical protein database. Then, proteins with no corresponding expressed transcript in the sample-matched transcriptome, and for which no specific peptide was detected (both conditions required), were removed. Peptides only mapping to that set of proteins were also removed. B Number of valid spectra and peptide identifications obtained from the full or reduced target-only database search (red and blue) or from the post hoc filtering strategy (orange), after 1% FDR control by BH procedure. C Quantification of protein ambiguity for the full or reduced database search (red and blue) or the post hoc filtering strategies (orange). Upper panel: total number of CCs obtained. Lower panel: percentage of specific peptides and single-protein CCs