Figure 6.

Nano-flow LC–MS/MS benchmarking of the P-VIS workflow using native and spliced peptides (spectrum comparison plus RT comparison; manual delta RT threshold = 0.5 min). Results are based on the combination of spectrum comparison and retention time comparison results. For RT comparison, the entire RT range was included, and a manual delta RT threshold of 0.5 min was used. Blue shading indicates that PSM_validator correctly identified the two peptides as either a match or mismatch. Red shading indicates that the program’s assessment was incorrect. Regions of the validation peptide that differ from the mock-biological peptide are underlined. Experiments are technical replicates (i.e., the same samples were run on three consecutive days). Rep = technical replicate. TP = true positive. TN = true negative. FP = false positive. FN = false negative. In cases where the analysis could not be completed, the reason is indicated as follows: a = in the mock-biological run, no spectrum satisfying minimum scoring requirements; b = in the validation run, no spectrum satisfying minimum scoring requirements (for this dataset, there were no instances where both runs lacked a satisfactory spectrum); c = too few ion pairs between the two spectra to complete Pearson analysis.