In vitro reconstitution of epigenetic reprogramming in the human germ line

M1-BTAG iPSCs or TET1-KO iPSCs were analyzed by 8% SDS-PAGE, followed by trypsin digestion and LC/MS/MS with an Orbitrap Fusion Lumos linked with an Ultimate 3000 pump and HTC-PAL autosampler. Acquired data files were processed using FragPipe v20.0 (MSFragger v3.8, Philosopher v5.0.0, IonQuant v1.9.8) for protein identification and quantitation. Peptides and proteins were identified by automated database searching against the human UniprotKB/Swissprot database (accessed on 2021/07/15) with settings of strict trypsin (C-terminal of K and R) specificity and the allowance for up to 2 missed cleavages. Carbamidomethylation of cysteine (C, +57.021465) was set as a fixed modification. Oxidation of methionine (M, +15.9949) and acetylation of protein N-terminus (Protein N-term, +42.0106) were set as variable modifications. A total of 2139 protein groups were identified.