This folder contains supplementary information for Oscar M Camacho thesis (Chapter 3) titled "Statistical developments for the identification of protein post-translational modifications using decoy amino acids"

The folder named "Data" contains the following:

 - GSB: GSB classification for Plasmodium and rice using all 3 pipelines (MQ, PD and TPP)
 
 - MQ: MaxQuant analysis at PSM and peptidoform level for Plasmodium and rice.
 
 - PD: Proteome Discoverer analysis at PSM and peptidoform level for Plasmodium and rice.
 
 - TPP: Trans-proteomic pipeline analysis at PSM and peptidoform level for Plasmodium and rice.
 
 - Musite: Musite predictions for Plasmodium and rice.
 
 The folder named "R functions" contains the following:
 
 - Binomial Scores Function Peptidoform level.R : Calculate binomial adjusted scores peptidoform level(TPP).
 - MQ Binomial Scores Function Peptidoform level MQ.R : Calculate binomial adjusted scores peptidoform level(MQ).
 - PD Binomial Scores Function Peptidoform level PD.R : Calculate binomial adjusted scores peptidoform level(PD).
 - CompScans_05pASTYtoAllpSTY.R : Compares scans of pASTY scores at 5% FLR vs all pSTY (TPP).
 - CompScans_05pASTYtoAllpSTY_MQ.R : Compares scans of pASTY scores at 5% FLR vs all pSTY (MQ).
 - CompScans_05pASTYtoAllpSTY_PD.R : Compares scans of pASTY scores at 5% FLR vs all pSTY (PD).
 - CompScans_95pSTYtoAllpASTY.R : Compares scans of pSTY scores above 0.95 vs all pASTY (TPP).
 - CompScans_95pSTYtoAllpASTY_MQ.R : Compares scans of pSTY scores above 0.95 vs all pASTY (MQ).
 - CompScans_95pSTYtoAllpASTY_PD.R : Compares scans of pSTY scores above 0.95 vs all pASTY (PD).
 - CompScansAllpASTYtoAllpSTY.R : Compares all pASTY matches to all pSTY (TPP).
 - MQ_CompScansAllpASTYtoAllpSTY : Compares all pASTY matches to all pSTY (MQ).
 - PD_CompScansAllpASTYtoAllpSTY : Compares all pASTY matches to all pSTY (PD).
 - FLR function Bin Adjusted.R : Calculates FLR for data from the TPP and PD pipeline.
 - FLR function Bin Adjusted_MQ : Calculates FLR for data from the MQ pipeline.
 - Function frequency of site MaxQuant.R : Function calculating the number of ocurrancies a site is observed in dataset (MQ).
 - Function frequency of site PDiscoverer.R : Function calculating the number of ocurrancies a site is observed in dataset (PD).
 - GBS_Function : Classified PTMs as gold, silver and bronze.
 
  The folder named "Tables and figures" contains the following:
 
 - Figure 15 and 16 folder : Outputs and code to create figures 15 and 16th in thesis.
 - Figure 17 folder : Outputs and code to create figures 17th in thesis.
 - Figure 20 folder : Outputs and code to create figures 20th in thesis.
 - Figure 23 folder : Outputs and code to create figures 23th in thesis.
 - Figure 25 folder : Outputs and code to create figures 25th in thesis.
 - Figure 26 folder : Outputs and code to create figures 26th in thesis.
 - Figure 27 folder : Outputs and code to create figures 27th in thesis.
 - "Peptidoform level analysis" folder : Peptidoform level analysis code for TPP, MQ and PD.
 - Table 16 folder: Code to create table 16 in thesis.
 - Table 17 folder: Code to create table 17 in thesis.
 - Table 18 folder: Code to create table 18 in thesis and output.
 
 
 
 
 
 
 
 
 

 
 