Conclusions:
• Optimization of PQD parameters for LC MS/MS analysis is important for reproducible and accurate rotein quantitation.
• The PQD fragmentation technique produces high quality MS/MS spectra with good signal to noise for TMT reporter ions.
• The accuracy of the TMT ratios was better than 19% on the protein level.
• Proteome Discoverer performs protein identification and protein quantitation using the MS/MS spectra generated by PQD. Reporter ion intensities of the MS/MS spectra were successfully used for peptide and protein quantitation.

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