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Fig. 3 | BMC Genomics

Fig. 3

From: A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

Fig. 3

NbD/NbDE datasets outperform the annotation of spectra in proteomics. a Percentage of annotated MS/MS spectra in total leaf extract samples. b Average number of unique peptides assigned per protein in the different datasets. a and b Means and standard error of the mean are shown for four biological replicates of total leaf extracts. c Mis-annotations of papain-like Cys proteases (PLCPs) detected by activity-based protein profiling [54]. Leaf extracts were labelled with activity-based probes for PLCPs and labelled proteins were purified and analysed by MS. Shown are the protein annotations found in the NbDE (top) Niben1.0.1 (middle) and curated datasets (bottom), highlighting mis-annotations (red) caused by partial transcripts, mis-annotation of exon-intron boundaries, and mis-assemblies

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