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.