to a false discovery rate (FDR) of less than 1%. Following spectral assignment, peptides were assembled into proteins, which were further filtered based on the combined probabilities of their constituent peptides to a final FDR of 1%. In cases of redundancy, shared peptides were assigned to the protein sequence based on parsimony. Reporter ions were quantified from MS2 or MS3 scans using an integration tolerance of 20 ppm with the most confident centroid setting.
