The mass range used for the XICs was the observed m/ z value±10 p.p.m. of the relevant peptide.
Data were collected over the 50 1990 mass to charge (m/z) range using the Waters Protein Expression MSE method, which alternates between low energy scans to survey the precursor ions and high collision energy scans to fragment all of the precursor ions.
For FTMS MS2 spectra, normal mass range was used, centroiding the data at 7500 resolution.
A set of 10 peaks that occurred in the majority of spectra and were evenly distributed across the whole mass range were used for internal calibration.
The instrument was calibrated with an external calibration using matrix dimers at m/z 379.0930 and des-Arg1-Bradykinin at m/z 904.4681 for the mass range 450 1,600 or using the Mass Standards Kit for Calibration of AB SCIEX TOF/TOF™ Instruments as default calibration.
Mass spectrometry data were acquired in positive and reflectron mode, mass range 600 1100 Da, using a neodymium-doped yttrium aluminum garnet (Nd YAG) laser with a 200-Hz repetition rate.
The use of the optimized automatic sprayer methods significantly increases the number of metabolites detected within a defined mass range, especially when using DHB.
Survey MS spectra were collected (m/z 400 to 1,500) for 1 second followed by three MS/MS measurements on the most intense parent ions (80 counts/second threshold, +2 to +4 charge state, and m/z 100 to 1,500 mass range for MS/MS), using the manufacturer's 'smart exit' and 'iTRAQ' settings.
Retention time range used for averaging mass spectra [min].
The representative MS/MS spectra for three selected fragments of αA- and αB- crystallin are presented in Figs. S7, S8, S9 in the ESM.> -wrap-foot> AA potential glycated lysine residues aRetention time range used for averaging mass spectra [min].
