Figure 4
From: PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
Phosphoprotein and -peptide identification results from the qualitative phosphoproteomics samples after manual compilation of the database search results, as well as after automatic processing with PhosFox. With manual compilation, 158 unique phosphoproteins for the case sample, and 154 unique phosphoproteins for the control sample were identified. With PhosFox, 611 unique phosphopeptides for the case sample, and 612 unique phosphopeptides for the control sample were identified, and 1380 phosphopeptides were identified from both control and case samples. The identical 1380 phosphopeptides across the control and case samples were discarded for further processing. The unique phosphopeptides resulted in identification of 426 unique phosphoproteins from the case, and 420 unique phosphoproteins from the control sample. From these, 151 proteins were identified in both samples with differences in phosphorylation sites.