Fig. 6.

Phosphoproteomic work flow. Graphical representation of the sample preparation, LC-MS³, and bioinformatic steps taken in the nuclear phosphoproteomic study. Ovals represent the sample or proteomic data. Shaded boxes represent the biochemical and computational methods that were applied to the sample or proteomic data. The work flow utilized 2 phosphopeptide isolation kits (IMAC and TiO₂ tips) to maximize phosphopeptide recovery and 3 phosphorylation site verification programs (Ascore, PLscore, and PhosphoScore) to ensure phosphosite validity.