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.

附加文件2：表S1 采用hybrid-PRM/DIA与数据非依赖采集（Data Independent Acquisition，DIA）技术监测的生物样本库黑色素瘤患者样本列表。表S2 jpt肿瘤相关抗原（Tumor-Associated Antigen，TAA）肽段组合（重标与轻标）概况。表S3 30种用作黑色素瘤1级/2级诊断标志物的AQUA（Absolute Quantitation peptide）肽段列表。表S4 185种TAA肽段加11种保留时间肽段的平行反应监测（Parallel Reaction Monitoring，PRM）排程列表。表S5 用于触发185种TAA肽段MSxPRM扫描的hybrid-PRM/DIA应用程序编程接口（Application Programming Interface，API）输入列表。表S6 用于触发179种TAA肽段MSxPRM扫描的hybrid-PRM/DIA API输入列表。表S7 用于触发120种TAA肽段MSxPRM扫描的hybrid-PRM/DIA API输入列表。表S8 用于触发60种TAA肽段MSxPRM扫描的hybrid-PRM/DIA API输入列表。表S9 用于触发30种黑色素瘤AQUA肽段MSxPRM扫描的hybrid-PRM/DIA API输入列表。表S10 30种黑色素瘤AQUA肽段加11种内标保留时间（iRT）肽段的PRM排程列表。表S11 65种1级与2级黑色素瘤标志物蛋白/蛋白组列表。表S12 95例患者样本中43种黑色素瘤标志物蛋白的定量蛋白矩阵，所有数值均经log10转换，为图S4热图的构建基础。图5B中讨论的蛋白以红色标注。