Mapping the MHC class I spliced immunopeptidome of cancer cells

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