A triple quadrupole mass spectrometer (QTRAP 5500; AB Sciex, Redwood, CA, US) was connected to a nano-ACQUITY UPLC system with a C18 column (100 μm×100 mm, 1.7-μm particle size; Waters). To inject the LC-MRM-MS system, a sample of 4 microliters containing 1 μg of peptides was used, and a linear gradient of buffer A (0.1% FA in H2O) combined with buffer B (0.1% FA in acetonitrile) was applied for 42 minutes. In order to obtain sensitive detection of peptide targets in biological samples, the acquisition parameters (CE, DP, EP, CEP, CXP) for each target peptide and the instrument settings were experimentally determined. Raw MRM analysis files (.wiff) were processed using Skyline software with the defined precursor (Q1) and fragment (Q3) mass list of the target peptides.

Each sample was subjected to triplicate measurements of LC-MRM-MS to obtain technical replicates.
The four datasets vary in the number of monitored peptides:

Dataset CKD includes 20 peptides

Dataset OSCC-1 includes 53 peptides

Dataset OSCC-2 includes 28 peptides

Dataset OSCC-3 includes 45 peptides

Each chromatogram comprises a light ion (target peptide) and a heavy ion (SIS peptide),
and the identity of peptides is represented by three distinct transitions (paired Q1/Q3).
The output files of the Skyline software in text format contain chromatograms and peak boundaries.