Mapping the MHC class I spliced immunopeptidome of cancer cells
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Fig. 1 (+ 2D GR-LCL) files: filteredSearchResults.xlsx. Listed are all peptides identified in the HCT116, HCC1143 and 2D GR-LCL MHC-I immunopeptidomes (spliced and non-spliced, 9-12mer sequences) with MS/MS scan numbers, retention times, mass characteristics and ion scores. Fig. 1C-E File: LyS-tryp_HCC1143_30KDa.RAW LysC/trypsin digestion of the HCC1143 protein sample (proteins > 30kDa) measured by Q Exactive Orbitrap Fig. 3C Folder: HCC1143_mutation_cosmic_database Mutations of the HCC1143 cell line as reported in the Cosmic database (version 17/8/2016) files: Mutations_in_sampleWed Aug 17 16-37-54 2016.csv Mutations_in_sampleWed Aug 17 16-38-01 2016.csv Mutations_in_sampleWed Aug 17 16-38-09 2016.csv Mutations_in_sampleWed Aug 17 16-38-18 2016.csv Fig. 3C-E Folder: HCT116_mutation_cosmic_database Mutations of the HCT116 cell line as reported in the Cosmic database (version 17/8/2016) files: Mutations_in_sampleWed Aug 17 17-09-53 2016.csv Fig. S5 Folder: in_vitro_digestions files: RAW files of the in vitro digestions (with or without proteasome) of the synthetic polypeptides mutCHMP7 and mutRBBP7 (see Table S6) and the target synthetic peptides’ run. The MS/MS of the identified neoepitopes are shown in Fig. S5. In particular: - “synthetic_peptides.RAW” is a mix containing also the synthetic peptides CHMP7[A324T]_316-325 and RBBP7[N17D]_12-20 - “mutCHMP7_20h.RAW” is the digestion (20h) of the synthetic substrate mutCHMP7_312-330 with purified proteasome - “mutCHMP7_20h_no-proteasome.RAW” is the digestion (20h) of the synthetic substrate mutCHMP7_312-330 without purified proteasome - “mutRBBP7_20h.RAW” is the digestion (20h) of the synthetic substrate mutRBBP7_6-25 with purified proteasome - “mutRBBP7_20h_no-proteasome.RAW” is the digestion (20h) of the synthetic substrate mutRBBP7_6-25 without purified proteasome The scripts for the MHC-I spliced peptides’ database generation Folder: TourDeForce
图1（附2D GR-LCL相关数据） 数据文件：filteredSearchResults.xlsx。 该文件收录了在HCT116、HCC1143及2D GR-LCL的主要组织相容性复合体I类（MHC-I）免疫肽组中鉴定到的所有肽段（包含剪接型与非剪接型9~12肽序列），并附带串联质谱（MS/MS）扫描编号、保留时间、质量特征及离子得分。 图1C~E 数据文件：LyS-tryp_HCC1143_30KDa.RAW 该文件对应经Q Exactive Orbitrap质谱仪检测的HCC1143蛋白质样品（分子量＞30kDa的蛋白组分）的LysC/胰蛋白酶酶解产物数据。 图3C 数据文件夹：HCC1143_mutation_cosmic_database 该文件夹收录了COSMIC数据库（版本2016年8月17日）中记录的HCC1143细胞系突变信息，包含以下数据文件： Mutations_in_sampleWed Aug 17 16-37-54 2016.csv Mutations_in_sampleWed Aug 17 16-38-01 2016.csv Mutations_in_sampleWed Aug 17 16-38-09 2016.csv Mutations_in_sampleWed Aug 17 16-38-18 2016.csv 图3C~E 数据文件夹：HCT116_mutation_cosmic_database 该文件夹收录了COSMIC数据库（版本2016年8月17日）中记录的HCT116细胞系突变信息，对应数据文件为： Mutations_in_sampleWed Aug 17 17-09-53 2016.csv 补充图S5 数据文件夹：in_vitro_digestions 该文件夹收录了合成多肽mutCHMP7与mutRBBP7（详见补充表S6）的体外酶解（添加或不添加纯化蛋白酶体）以及目标合成肽段上机检测的RAW格式数据文件，所鉴定新表位的串联质谱（MS/MS）结果详见补充图S5。具体如下： - "synthetic_peptides.RAW"：同时包含合成肽段CHMP7[A324T]_316-325与RBBP7[N17D]_12-20的混合样品检测数据 - "mutCHMP7_20h.RAW"：经纯化蛋白酶体酶解20小时的合成底物mutCHMP7_312-330的检测数据 - "mutCHMP7_20h_no-proteasome.RAW"：未添加纯化蛋白酶体、酶解20小时的合成底物mutCHMP7_312-330的检测数据 - "mutRBBP7_20h.RAW"：经纯化蛋白酶体酶解20小时的合成底物mutRBBP7_6-25的检测数据 - "mutRBBP7_20h_no-proteasome.RAW"：未添加纯化蛋白酶体、酶解20小时的合成底物mutRBBP7_6-25的检测数据 MHC-I剪接肽段数据库生成脚本 数据文件夹：TourDeForce
