Raw data was searched using the SEQUEST search engine within the Proteome Discoverer software platform, version 1.4 (Thermo Fisher), using the SwissProt human database that was downloaded in December of 2015. Trypsin was selected as the enzyme allowing up to two missed cleavages, with an MS1 mass tolerance of 10 ppm, and an MS2 mass tolerance of 25 mmu. Carbamidomethyl was set as a fixed modification, while oxidation of methionine was set as a variable modification. Percolator was used as the FDR calculator, filtering out peptides which had a q-value > 0.0169. The Mascot scores of individual peptides were calculated as the absolute probability that the observed peptide match is a random event when matching spectra to all the expected spectra of a given proteome70. The Mascot score of a given peptide is equal to: −10 × Log10(P), where P is the absolute probability. The Mascot scores for individual proteins were then calculated based upon the summation of the individual peptides for all peptides matching a given protein. The samples analyzed by LC-MS include purifications from control cell lines, Strep-METTL2A, Strep-METTL2B, and Strep-METTL6. The LC-MS analysis was performed once with each sample.
