Supplementary Figure 4: Peptide identifications (score >100) across different acquisition methods

(a) Venn diagram for the comparison of identifications with an Andromeda Score >100 across five major fragmentation types. The upper bar chart displays the number of peptide identifications for each fragmentation type, the lower bar chart shows peptide identifications only if the corresponding method reached a score of at least 90% of the highest score observed for that peptide (indicating the number of peptides for which the respective fragmentation technique gave the best identification result). We note that even though the various ETD versions were less successful than CID or HCD, there are still thousands of peptides for which ETD is the best fragmentation technique. (d) Venn diagram for the comparison of identifications using different HCD collision energies with an Andromeda Score >100. The upper bar chart displays peptide identifications for every collision energy, the lower bar chart shows peptide identifications only if the corresponding collision energy experiment reached a score of at least 90% of the highest score observed for that peptide.