Additional file 2 of Simultaneous targeted and discovery-driven clinical proteotyping using hybrid-PRM/DIA

Additional file 2: Table S1. List of biobanked melanoma patient samples monitored with hybrid-PRM/DIA and DIA. Table S2. Overview of jpt TAA peptide panel (heavy and light). Table S3. List of 30 AQUA peptides used as melanoma level-1/2 diagnostic markers. Table S4. PRM scheduling list of the 185 TAA peptides plus 11 retention time peptides. Table S5. Hybrid-PRM/DIA API input list for triggering of MSxPRM scans of the 185 TAA peptides. Table S6. Hybrid-PRM/DIA API input list for triggering of MSxPRM scans of the 179 TAA peptides. Table S7. Hybrid-PRM/DIA API input list for triggering of MSxPRM scans of the 120 TAA peptides. Table S8. Hybrid-PRM/DIA API input list for triggering of MSxPRM scans of the 60 TAA peptides. Table S9. Hybrid-PRM/DIA API input list for triggering of MSxPRM scans of the 30 melanoma AQUA peptides. Table S10. PRM scheduling list of the 30 melanoma AQUA peptides plus 11 iRT peptides. Table S11. List of the 65 level-1 and level-2 melanoma marker proteins/protein groups. Table S12. Quantitative protein matrix over 43 melanoma marker proteins in 95 patient samples. Values are log10-transformed and the basis of the heatmap in Fig. S4. The proteins discussed in Fig. 5B are indicated in red.