Phosphoproteomic data quality and reproducibility. A Distribution of Andromeda scores of the identified phosphorylated peptides show that most peptides were identified with high scores with a median score of 130. B Distribution of localization probabilities of identified phosphorylation sites. The median probability wasâ~â0.97. C Assessment of reproducibility between the four biological replicates carried out with SILAC label swapping shows optimal reproducibility among the forward and reverse experiments. The correlation scores are indicated in each scatter plot. (PDF 1803 kb
Additional file 1: Table S1. Phosphoproteomics data for peptides with large fold-changes at the 1- a...
Table S1. Positively-charged patches size profile of rHuEPO WT from the charged patch calculator. Co...
Overlap in identification of phosphorylated proteins/phospho-sites and distribution of measured prot...
Enrichment of cellular component terms among the different categories. (XLSX 12 kb
List of ANXA1-responsive phosphorylation sites in mammary epithelial cells from ANXA1-heterozygous a...
Quantitative reproducibility of biological replicates employed for phosphoproteomics and proteomics ...
Reproducibility of measured protein ratios within three technical replicates. (A) Phosphoproteome me...
(A) Venn diagram comparison of three different reported phosphoproteome data sets from melanoma-deri...
MA Plot. This MA plot shows the data before (a) and after (b) transformation. The variances of the d...
Table S1. The table is organized in the following spreadsheets: Spreadsheet “All Phosphopeptides”: T...
Figure S1. Immunoblotting analysis with antibodies against total phosphotyrosines on lysates derived...
RC-C HCL clustering using qPSP using various alpha thresholds (A) Using top and bottom ranked protei...
Table S2. The file is organized into the following spreadsheets: Spreadsheet “Cell. & Biol. processe...
Figure S2. Cellular components and protein classes associated with the 50 proteins identified. Resul...
Figure S1. PTEN protein abundance of breast cancer cell lines. (A) Western blots showing PTEN and ac...
Additional file 1: Table S1. Phosphoproteomics data for peptides with large fold-changes at the 1- a...
Table S1. Positively-charged patches size profile of rHuEPO WT from the charged patch calculator. Co...
Overlap in identification of phosphorylated proteins/phospho-sites and distribution of measured prot...
Enrichment of cellular component terms among the different categories. (XLSX 12 kb
List of ANXA1-responsive phosphorylation sites in mammary epithelial cells from ANXA1-heterozygous a...
Quantitative reproducibility of biological replicates employed for phosphoproteomics and proteomics ...
Reproducibility of measured protein ratios within three technical replicates. (A) Phosphoproteome me...
(A) Venn diagram comparison of three different reported phosphoproteome data sets from melanoma-deri...
MA Plot. This MA plot shows the data before (a) and after (b) transformation. The variances of the d...
Table S1. The table is organized in the following spreadsheets: Spreadsheet “All Phosphopeptides”: T...
Figure S1. Immunoblotting analysis with antibodies against total phosphotyrosines on lysates derived...
RC-C HCL clustering using qPSP using various alpha thresholds (A) Using top and bottom ranked protei...
Table S2. The file is organized into the following spreadsheets: Spreadsheet “Cell. & Biol. processe...
Figure S2. Cellular components and protein classes associated with the 50 proteins identified. Resul...
Figure S1. PTEN protein abundance of breast cancer cell lines. (A) Western blots showing PTEN and ac...
Additional file 1: Table S1. Phosphoproteomics data for peptides with large fold-changes at the 1- a...
Table S1. Positively-charged patches size profile of rHuEPO WT from the charged patch calculator. Co...
Overlap in identification of phosphorylated proteins/phospho-sites and distribution of measured prot...