Figure 3
From: msmsEval: tandem mass spectral quality assignment for high-throughput proteomics
msmsEval highlights strong candidates for modified peptide spectra. The observed p(+|D) versus predicted p(+|D) values for 22 runs of the ISB dataset (A) were plotted using binned sets of 100 spectra (i.e. the fraction of the 100 spectra that were observed to be identifiable versus the mean p(+|D)). Observed p(+|D) values calculated using SEQUEST identifications (x), SEQUEST and MSAlignment/InsPecT identifications (â—†), and SEQUEST and MSAlignment/InsPecT identifications as well as the additional assignments described in the text (o), are indicated. A pie chart (B) shows the absolute numbers and percentages of spectra from the ISB dataset with predicted p(+|D) > 0.9 that were identified by SEQUEST/MSAlignment/InsPecT, those that were additionally identified by msmsEval, and those that remain unidentified. In total, 83.9% of spectra with p(+|D) > 0.9 were identified.