Because different phosphosites in a protein may trigger either protein activation or inactivation, we used phosphosite instead of phosphoprotein as unit for quantification.
In this study, we also found an upregulation of Ser583 on PML in drug resistant cell lines, a new phosphosite which has not been previously described.
Ser23 of Lamin B1 (LMNB1) was also identified as an upregulated phosphosite in the resistant cell lines in this study.
2.1.3, Proteome Software Inc.) was used to annotate phosphosites located in MS/MS spectra.
Accordingly, a total of 9,585 unique phosphopeptides with 10,091 unique phosphosites were identified (see Supplementary Table 1 in Supplementary Material available online at http://dx.doi.org/10.1155/2014/390781).
Phosphosites Confirmation and Label Free Quantification.
Written for both new and experienced scientists, the text covers two-dimensional gel electrophoresis and protein phosphorylation, enrichment of phosphoproteins and peptides,quantitative analysis of phosphorylation by labeling and MS analysis, antibody and kinase arrays, bioinformatics and phosphosite
prediction, identification of phosphoproteins by mass spectrometry, and various chemical tagging strategies.