Figure 5

A pair-wise comparison of peptide masses overlapping with identified protein GI's, each time between the peptide profile matrices from two MS1 software packages. All masses are sequenced and identified, including the non-overlapping masses in the individual packages. A comparison matrix was constructed by Peptrix using an artificial grid of 20275 masses between 1600 and 2400 Da with distances of 20 ppm between the masses. Peak masses from two peptide profile matrices identified with protein GI's for the software packages Peptrix, Sieve™, Progenesis™ and msInspect were matched with the comparison matrix grid, using a mass window with 10 ppm in two directions and a total distance of 20 ppm.