Table II

Identified phosphopeptides using directed LC-MS/MS

LC-MS/MS runaNo. of peptides identifiedbNo. of phosphopeptides identifiedbNo. of phosphorylation sites identifiedbPercentage of phosphopeptides identifiedb
1 (DDA 2+)74265567888.27
2 (DDA >2+)1,08594999787.47
3 (INL-1)1,4391,2541,34787.14
4 (INL-2)1,6211,4051,52186.67
5 (INL-NL)1,7211,5001,62887.16
  • a Runs 1 (DDA 2+) and 2 (DDA >2+), only doubly or higher charged peptide ions, respectively, were allowed to trigger CID by DDA. Runs 3 (INL-1) and 4 (INL-2), directed LC-MS/MS of unsequenced features extracted from runs 1 and 2. Run 5 (INL-NL), directed LC-MS/MS of unassigned neutral loss-showing precursors.

  • b Numbers calculated from Bioworks 3.2 search results using an in-house software tool (25).