## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width=8, fig.height=8 ) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("MSstatsPTM") ## ----message=FALSE, warning=FALSE--------------------------------------------- library(MSstatsPTM) library(MSstats) ## ----maxq, eval=TRUE---------------------------------------------------------- # TMT experiment head(maxq_tmt_evidence) head(maxq_tmt_annotation) msstats_format_tmt = MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence, annotation=maxq_tmt_annotation, fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"), fasta_protein_name="uniprot_ac", mod_id="\\(Phospho \\(STY\\)\\)", use_unmod_peptides=TRUE, labeling_type = "TMT", which_proteinid_ptm = "Proteins") head(msstats_format_tmt$PTM) head(msstats_format_tmt$PROTEIN) # LF experiment head(maxq_lf_evidence) head(maxq_lf_annotation) msstats_format_lf = MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence, annotation=maxq_lf_annotation, fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"), fasta_protein_name="uniprot_ac", mod_id="\\(Phospho \\(STY\\)\\)", use_unmod_peptides=TRUE, labeling_type = "LF", which_proteinid_ptm = "Proteins") head(msstats_format_lf$PTM) head(msstats_format_lf$PROTEIN) ## ----fragpipe, eval=TRUE------------------------------------------------------ head(fragpipe_input) head(fragpipe_annotation) head(fragpipe_input_protein) head(fragpipe_annotation_protein) msstats_data = FragPipetoMSstatsPTMFormat(fragpipe_input, fragpipe_annotation, fragpipe_input_protein, fragpipe_annotation_protein, mod_id_col = "STY", localization_cutoff=.75, remove_unlocalized_peptides=TRUE) head(msstats_data$PTM) head(msstats_data$PROTEIN) ## ----pd, eval=TRUE------------------------------------------------------------ head(pd_psm_input) head(pd_annotation) msstats_format = PDtoMSstatsPTMFormat(pd_psm_input, pd_annotation, system.file("extdata", "pd_fasta.fasta", package="MSstatsPTM"), use_unmod_peptides=TRUE, which_proteinid = "Master.Protein.Accessions") head(msstats_format$PTM) head(msstats_format$PROTEIN) ## ----Spectronaut, eval=TRUE--------------------------------------------------- head(spectronaut_input) head(spectronaut_annotation) msstats_input = SpectronauttoMSstatsPTMFormat(spectronaut_input, annotation=spectronaut_annotation, fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"), use_unmod_peptides=TRUE, mod_id = "\\[Phospho \\(STY\\)\\]", fasta_protein_name = "uniprot_iso" ) head(msstats_input$PTM) head(msstats_input$PROTEIN) ## ----raw_data, eval = FALSE--------------------------------------------------- # # Add site into ProteinName column # raw_ptm_df$ProteinName = paste(raw_ptm_df$ProteinName, # raw_ptm_df$Site, sep = "_") # # # Run MSstats Converters # PTM_data = MSstats::DIANNtoMSstatsFormat(raw_ptm_df, annotation) # PROTEIN_data = MSstats::DIANNtoMSstatsFormat(raw_protein_df, annotation) # # # Combine into one list # msstatsptm_input_data = list(PTM = PTM_data, PROTEIN = PROTEIN_data) ## ----summarize, message=FALSE, warning=FALSE---------------------------------- MSstatsPTM.summary = dataSummarizationPTM(raw.input, verbose = FALSE, use_log_file = FALSE, append = FALSE) head(MSstatsPTM.summary$PTM$ProteinLevelData) head(MSstatsPTM.summary$PROTEIN$ProteinLevelData) ## ----qcplot, message=FALSE, warning=FALSE------------------------------------- dataProcessPlotsPTM(MSstatsPTM.summary, type = 'QCPLOT', which.PTM = "allonly", address = FALSE) ## ----profileplot, message=FALSE, warning=FALSE-------------------------------- dataProcessPlotsPTM(MSstatsPTM.summary, type = 'ProfilePlot', which.Protein = "Q9Y6C9", address = FALSE) ## ----model, message=FALSE, warning=FALSE-------------------------------------- # Specify contrast matrix comparison = matrix(c(-1,0,1,0),nrow=1) row.names(comparison) = "CCCP-Ctrl" colnames(comparison) = c("CCCP", "Combo", "Ctrl", "USP30_OE") MSstatsPTM.model = groupComparisonPTM(MSstatsPTM.summary, data.type = "LabelFree", contrast.matrix = comparison, use_log_file = FALSE, append = FALSE, verbose = FALSE) head(MSstatsPTM.model$PTM.Model) head(MSstatsPTM.model$PROTEIN.Model) head(MSstatsPTM.model$ADJUSTED.Model) ## ----volcano, message=FALSE, warning=FALSE------------------------------------ groupComparisonPlotsPTM(data = MSstatsPTM.model, type = "VolcanoPlot", FCcutoff= 2, logBase.pvalue = 2, address=FALSE) ## ----heatmap, message=FALSE, warning=FALSE------------------------------------ groupComparisonPlotsPTM(data = MSstatsPTM.model, type = "Heatmap", which.PTM = 1:30, address=FALSE) ## ----sample_size, message=FALSE, warning=FALSE-------------------------------- # Specify contrast matrix sample_size = designSampleSizePTM(MSstatsPTM.model, c(2.0, 2.75), FDR = 0.05, numSample = TRUE, power = 0.8) head(sample_size) ## ----sample_size_plot, message=FALSE, warning=FALSE--------------------------- MSstats::designSampleSizePlots(sample_size)