Mass spectrometry analysis

We downloaded raw mass spectrometry files from the CPTAC data portal (https://cptc-xfer.uis.georgetown.edu/publicData/Phase_II_Data/TCGA_Colorectal_Cancer/), in.raw and.mzML formats, for n = 96 samples from the colon adenocarcinoma TCGA cohort. For matching cases, patient level curated mutation annotation files were obtained from TCGA GDAC Firehose (2016_01_28 release) (https://gdac.broadinstitute.org/). Fs-indel mutations were filtered from mutation annotation files, and in total n = 81 patients had both mass spectrometry data coupled with fs-indel mutational events. All mutated peptide sequences, resulting from frameshift mutation events, were calculated and used as a custom search library. Mass spectral searches were conducted using the Mascot search engine (v2.3.1)³⁷, with mutated peptide sequences appended to the known human proteome, in FASTA file format. The following settings were used: Fixed modifications: none; Variable modifications: Oxidation (M),Carbamidomethyl (C),Acetyl (N-term); MSMS tolerance: 0.5 Da; MS tolerance: 2 Da and Enzyme: non-specific.