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. Author manuscript; available in PMC: 2011 Jun 4.
Published in final edited form as: J Proteome Res. 2010 Jun 4;9(6):3103–3107. doi: 10.1021/pr1000225

Figure 3.

Figure 3

Intramolecular phosphate transfer does not appreciably affect site localization in synthetic peptide libraries. Each library was analyzed in triplicate by LC-MS/MS techniques where back-to-back CID and ETD spectra were collected for each selected phosphopeptide ion. Peptide identifications were filtered to <0.5% FDR. Data are shown as the mean of both libraries (triplicate analysis summed) with error bars at the minimum and maximum values. (A) ETD identified 10.1 % more peptides from these highly basic libraries. (B) CID and ETD are suited to different populations of charge states. (C) The fraction of incorrect site assignments either due to chance or to intramolecular phosphate transfer is very small. ETD is not significantly more reliable than CID at site localization in these known-site synthetic peptide libraries.