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(A) Peptide spectra matches (PSMs), (B) distinct peptides and (C) protein groups from the raw files for the comparison of OT- and IT-type detection using the back-to-back strategy (HCD-IT vs. HCD-OT). Six different MS data interpretation approaches were used in this study by combining SEQUEST or Mascot with different post-processing methods such as score-based, PeptideProphet, and Percolator.
