Proteomic Analysis of Human Samples

Data were processed automatically using Mascot Distiller software (version 2.7.1.0, Matrix Science). Peptides and proteins were identified using Mascot (version 2.6) through concomitant searches against Swiss-Prot (Homo sapiens taxonomy, downloaded in November 2019), a classical contaminants database (homemade), and their corresponding reversed databases. Trypsin/P was chosen as enzyme, and a maximum of two missed cleavages was allowed. Precursor and fragment mass error tolerances were set to 10 ppm and 25 mmu, respectively. Peptide modifications allowed during the search were: (1) cysteine carbamidomethylation (fixed); (2) acetylation of the protein’s N-terminus (variable), and (3) methionine oxidation (variable). Proline software (version 2.1) [29 (link)] was used to merge data for all patients. After merging, results were filtered: conserving rank 1 peptide-spectrum matches with a minimal length of 7 amino acids and a minimal Mascot peptide score of 25. With these parameters, the False Discovery Rate (FDR) for peptide/spectrum match identifications was below 1% according to the target-decoy approach. A minimum of two peptides was required for a protein group to be identified. Proline was then used to perform MS1-based label-free quantification of the protein groups identified, based on their specific peptide abundances (Supp. Table 1).