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Description of Additional Supplementary Files
File Name: Supplementary Data 1
Description: R code for phosphorylation stoichiometry calculation via 3DMM. This R script
file contains the R code needed to perform the 3DMM phosphorylation stoichiometry
calculation for Fig. 6.
File Name: Supplementary Data 2
Description: Example data for 3DMM in Fig. 6. This compressed file contains the
modificationspecificpeptides.txt output from MaxQuant and the
HumanAndYeastProtIdentifiers.txt to differentiate between human and yeast proteins, both
of which are needed to recreate the analysis in Fig. 6 with the R code in Supplementary Data
1.
File Name: Supplementary Data 3
Description: Overview of MS raw files and MaxQuant configuration settings. This xlsx-file
features an overview of all MS raw files, their association with the Figures and MaxQuant
configuration settings.
File Name: Supplementary Data 4
Description: Tools for signal-to-noise extraction in Fig. 1. This Perl script file contains the
code to read out TMT reporter ion signal-to-noise ratios from raw data after processing
using raxport.exe.
File Name: Supplementary Data 5
Description: Biological benchmark phosphorylation site intensities and SAM regulation.
This xslx-file features all intensities and SAM-test statistics of the biological benchmark
dataset in Fig. 3.
File Name: Supplementary Data 6
Description: Kinase motif and GO-term enrichment data. This xlsx-file features all enriched
kinase motifs and GO-terms from Fig. 4 and Supplementary Fig. 4/6.