Aflibercept Fc-fusion protein was denatured and reduced in 8 M urea and 2 mM neutralized Tris(2-carboxyethyl)phosphine at room temperature for 30 minutes. Next, the sample solution was diluted 10-fold using 25 mM Tris–HCl (pH 8.0) and digested using modified trypsin at 37°C for 16 hours. The proteolytic reaction was quenched by adding trifluoroacetic acid to a final concentration of 0.5%. The peptide solution was purified using a MonoSpin C18 reversed-phase column (GL Science, Tokyo, Japan). The eluting solution was evaporated in a centrifugal evaporator, and peptides were reconstituted in 0.1% formic acid (FA). Structures of tryptic aflibercept peptides were analyzed by high-resolution liquid chromatography–quadrupole ion-trap time-of-flight (QTOF) MS (Nexera Mikros high-performance microflow liquid chromatography and LCMS-9030; Shimadzu). LC-MS conditions were as follows: solvent A, 0.1% aqueous FA; solvent B, 80% acetonitrile with 0.1% FA; trap column, L-column2 ODS analytical columns, 0.3 × 5 mm, 3-µm resin, 10-nm pore (Chemicals Evaluation and Research Institute, Tokyo, Japan); separation column, L-column2 ODS analytical columns, 0.3 × 150 mm, 2 µm resin, 10 nm pore (Chemicals Evaluation and Research Institute); column temperature, 40°C; and flow rate, 5 µL/min. The gradient program was as follows: 0 to 10 minutes, %B = 0; 10 to 95 minutes, %B = 0 to 40 gradient; 95 to 105 minutes, %B = 40 to 100 gradient; 100 to 115 minutes, %B = 100; 115 to 130 minutes, %B = 0. MS and MS/MS spectra were obtained using a desolvation line, interface, and heat block at 200°C, 100°C, and 250°C, respectively. Nebulizer nitrogen gas flow was set to 1 L/min. The flow rate of heating gas was 3 L/min. The electrode of the electrospray ionization (ESI) interface was set to 3 kV. Pulse times for MS and MS/MS were 194 µs and 154 µs, respectively. Ion accumulation time was set to 100 ms for MS and 80 ms for MS/MS. MS/MS analysis was performed using the intensity-dependent top-12 MS/MS per scan based on data-dependent acquisition. The precursor MS was set from m/z 300 to 800, and fragments were set from m/z 200 to 1200. Ion valency was set to range between +2 and +6. The electrode of the collision-induced dissociation (CID) cell was set at −25 ± 5 V, with argon gas pressure at 250 kPa. Precursor and fragment ions were assigned using Mascot Distiller 2.6.2 peak processing software (Matrix Science, London, UK), and PEAKS Studio Xplus software (Bioinformatics Solutions, Waterloo, Canada), using the in-house FASTA database of aflibercept and other monoclonal antibody sequence information. The allowance of peptide m/z tolerance was set to within 50 ppm for precursor ions and 50 mDa for fragment ions.