Figure 2 Results of the database search for the UPS2 standard kit using MSFragger.
Sample A11-12042 is always shown in blue and sample A11-12043 is always shown in red. (A) Venn-diagram with the number of identified peptides in both samples with percentages between brackets. (B)Venn-diagram with the number of identified proteins in both samples with percentages between brackets. (C) A bar plot with the percentage of proteins detected for both samples for all 6 concentrations present in the UPS2 standard kit. (D) Boxplots showing the coverage of the proteins in the UPS2 standard kit at each concentration for both samples.

Benchmark dataset

The MS1 isotope distribution benchmark dataset can be found in Supplementing Information 2. The complete workflow resulted in 138.111 possible MS1 isotope distributions, 70.593 identifications in sample A11-12042 and 67.518 identifications in A11-12043. There were 127.646 peptide isotope distributions with 2 or more peaks and 10.465 peptide isotope distributions consisting only out of the monoisotopic peak. Isotope distributions with 2 isotope peaks (30.706 identifications) and isotope distributions with 3 isotope peaks (30.873) occurred the most (Table 2).
Table 2 Amount of extracted MS1 identifications with their maximum number of isotope peaks per sample.