MSstatsPTM TMT Workflow

Devon Kohler (kohler.d@northeastern.edu)

2023-02-28

library(MSstatsPTM)

This Vignette provides an example workflow for how to use the package MSstatsPTM for a TMT dataset.

Installation

To install this package, start R (version “4.0”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSstatsPTM")

1. Workflow

1.1 Raw Data Format

Note: We are actively developing dedicated converters for MSstatsPTM. If you have data from a processing tool that does not have a dedicated converter in MSstatsPTM please add a github issue https://github.com/Vitek-Lab/MSstatsPTM/issues and we will add the converter.

The first step is to load in the raw dataset for both the PTM and Protein datasets. Each dataset can formatted using dedicated converters in MSstatsPTM, such as MaxQtoMSstatsPTMFormat, or converters from base MSstatsTMT such as PDtoMSstatsTMTFormat, MaxQtoMSstatsTMTFormat, SpectroMinetoMSstatsTMTFormat, ect. If using converters from MSstatsTMT note they will need to be run both on the global protein and PTM datasets.

Please note for the PTM dataset, both the protein and modification site (or peptide), must be added into the ProteinName column. This allows for the package to summarize to the peptide level, and avoid the off chance there are matching peptides between proteins. For an example of how this can be done please see the code below.

1.1.1 Raw Data Converter

The output of the converter is a list with two formatted data.tables. One each for the PTM and Protein datasets.

Given there is not a dedicated MSstatsPTM converter for the processing tool, base MSstats converters can be used as follows. Please note ProteinName column must be a combination of the Protein Name and sitename.

Both of these conversion methods will output the same results.

1.2 Summarization - dataSummarizationPTM_TMT

After loading in the input data, the next step is to use the dataSummarizationPTM_TMT function This provides the summarized dataset needed to model the protein/PTM abundance. The function will summarize the Protein dataset up to the protein level and will summarize the PTM dataset up to the peptide level. There are multiple options for normalization and missing value imputation. These options should be reviewed in the package documentation.

#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   2%
  |                                                                            
  |==                                                                    |   3%
  |                                                                            
  |===                                                                   |   5%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |======                                                                |   8%
  |                                                                            
  |=======                                                               |   9%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |========                                                              |  12%
  |                                                                            
  |=========                                                             |  13%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  15%
  |                                                                            
  |===========                                                           |  16%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  21%
  |                                                                            
  |===============                                                       |  22%
  |                                                                            
  |================                                                      |  23%
  |                                                                            
  |=================                                                     |  24%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |====================                                                  |  28%
  |                                                                            
  |====================                                                  |  29%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |======================                                                |  31%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |========================                                              |  35%
  |                                                                            
  |=========================                                             |  36%
  |                                                                            
  |==========================                                            |  37%
  |                                                                            
  |===========================                                           |  38%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |============================                                          |  41%
  |                                                                            
  |=============================                                         |  42%
  |                                                                            
  |==============================                                        |  43%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |================================                                      |  45%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |=================================                                     |  48%
  |                                                                            
  |==================================                                    |  49%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================                                  |  51%
  |                                                                            
  |=====================================                                 |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  55%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |========================================                              |  57%
  |                                                                            
  |=========================================                             |  58%
  |                                                                            
  |==========================================                            |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  62%
  |                                                                            
  |============================================                          |  63%
  |                                                                            
  |=============================================                         |  64%
  |                                                                            
  |==============================================                        |  65%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |================================================                      |  69%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |==================================================                    |  71%
  |                                                                            
  |==================================================                    |  72%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  76%
  |                                                                            
  |======================================================                |  77%
  |                                                                            
  |=======================================================               |  78%
  |                                                                            
  |=======================================================               |  79%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |===========================================================           |  84%
  |                                                                            
  |===========================================================           |  85%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  87%
  |                                                                            
  |==============================================================        |  88%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |===============================================================       |  91%
  |                                                                            
  |================================================================      |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  95%
  |                                                                            
  |====================================================================  |  97%
  |                                                                            
  |====================================================================  |  98%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===                                                                   |   4%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |==========                                                            |  15%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |==========================                                            |  37%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |==================================                                    |  48%
  |                                                                            
  |====================================                                  |  52%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |============================================                          |  63%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |============================================================          |  85%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |===================================================================   |  96%
  |                                                                            
  |======================================================================| 100%
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   2%
  |                                                                            
  |==                                                                    |   4%
  |                                                                            
  |===                                                                   |   5%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |======                                                                |   8%
  |                                                                            
  |=======                                                               |   9%
  |                                                                            
  |=======                                                               |  11%
  |                                                                            
  |========                                                              |  12%
  |                                                                            
  |=========                                                             |  13%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  15%
  |                                                                            
  |============                                                          |  16%
  |                                                                            
  |============                                                          |  18%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  21%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |================                                                      |  24%
  |                                                                            
  |=================                                                     |  25%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |====================                                                  |  28%
  |                                                                            
  |=====================                                                 |  29%
  |                                                                            
  |=====================                                                 |  31%
  |                                                                            
  |======================                                                |  32%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |=========================                                             |  35%
  |                                                                            
  |==========================                                            |  36%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |===========================                                           |  39%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |==============================                                        |  42%
  |                                                                            
  |==============================                                        |  44%
  |                                                                            
  |===============================                                       |  45%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |==================================                                    |  48%
  |                                                                            
  |===================================                                   |  49%
  |                                                                            
  |===================================                                   |  51%
  |                                                                            
  |====================================                                  |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |=======================================                               |  55%
  |                                                                            
  |========================================                              |  56%
  |                                                                            
  |========================================                              |  58%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  61%
  |                                                                            
  |============================================                          |  62%
  |                                                                            
  |============================================                          |  64%
  |                                                                            
  |=============================================                         |  65%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |================================================                      |  68%
  |                                                                            
  |=================================================                     |  69%
  |                                                                            
  |=================================================                     |  71%
  |                                                                            
  |==================================================                    |  72%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  75%
  |                                                                            
  |======================================================                |  76%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |=======================================================               |  79%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |==========================================================            |  82%
  |                                                                            
  |==========================================================            |  84%
  |                                                                            
  |===========================================================           |  85%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  87%
  |                                                                            
  |==============================================================        |  88%
  |                                                                            
  |===============================================================       |  89%
  |                                                                            
  |===============================================================       |  91%
  |                                                                            
  |================================================================      |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  95%
  |                                                                            
  |====================================================================  |  96%
  |                                                                            
  |====================================================================  |  98%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   2%
  |                                                                            
  |===                                                                   |   4%
  |                                                                            
  |===                                                                   |   5%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |======                                                                |   8%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |========                                                              |  12%
  |                                                                            
  |=========                                                             |  13%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  16%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |=============                                                         |  18%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  22%
  |                                                                            
  |================                                                      |  23%
  |                                                                            
  |=================                                                     |  24%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |===================                                                   |  28%
  |                                                                            
  |====================                                                  |  29%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |======================                                                |  31%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |========================                                              |  35%
  |                                                                            
  |=========================                                             |  36%
  |                                                                            
  |==========================                                            |  37%
  |                                                                            
  |===========================                                           |  39%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |==============================                                        |  42%
  |                                                                            
  |==============================                                        |  43%
  |                                                                            
  |===============================                                       |  45%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |==================================                                    |  48%
  |                                                                            
  |===================================                                   |  49%
  |                                                                            
  |===================================                                   |  51%
  |                                                                            
  |====================================                                  |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |=======================================                               |  55%
  |                                                                            
  |========================================                              |  57%
  |                                                                            
  |========================================                              |  58%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  61%
  |                                                                            
  |============================================                          |  63%
  |                                                                            
  |=============================================                         |  64%
  |                                                                            
  |==============================================                        |  65%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |================================================                      |  69%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |==================================================                    |  71%
  |                                                                            
  |===================================================                   |  72%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |=====================================================                 |  76%
  |                                                                            
  |======================================================                |  77%
  |                                                                            
  |=======================================================               |  78%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |=========================================================             |  82%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |===========================================================           |  84%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  87%
  |                                                                            
  |==============================================================        |  88%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |================================================================      |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  95%
  |                                                                            
  |===================================================================   |  96%
  |                                                                            
  |====================================================================  |  98%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%

The summarize function returns a list with PTM and Protein summarization information.

1.2.1 QCPlot

Once summarized, MSstatsPTM provides multiple plots to analyze the experiment. Here we show the quality control boxplot. The first plot shows the modified data and the second plot shows the global protein dataset.

1.2.2 Profile Plot

Here we show a profile plot. Again the top plot shows the modified peptide, and the bottom shows the overall protein.

1.3 Modeling - groupComparisonPTM

After summarization, the summarized datasets can be modeled using the groupComparisonPTM function. This function will model the PTM and Protein summarized datasets, and then adjust the PTM model for changes in overall protein abundance. The output of the function is a list containing these three models named: PTM.Model, PROTEIN.Model, ADJUSTED.Model.


# Specify contrast matrix
comparison <- matrix(c(1,0,0,-1,0,0,
                       0,1,0,0,-1,0,
                       0,0,1,0,0,-1,
                       1,0,-1,0,0,0,
                       0,1,-1,0,0,0,
                       0,0,0,1,0,-1,
                       0,0,0,0,1,-1),nrow=7, ncol=6, byrow=TRUE)

# Set the names of each row
row.names(comparison)<-c('1-4', '2-5', '3-6', '1-3', 
                         '2-3', '4-6', '5-6')
colnames(comparison) <- c('Condition_1','Condition_2','Condition_3',
                          'Condition_4','Condition_5','Condition_6')
MSstatsPTM.model <- groupComparisonPTM(MSstatsPTM.summary,
                                       data.type = "TMT",
                                       contrast.matrix = comparison,
                                       use_log_file = FALSE, append = FALSE)
#> INFO  [2023-02-28 17:10:10] Design: 2 mixtures.
#> INFO  [2023-02-28 17:10:10] Design: 1 MS run per mixture.
#> INFO  [2023-02-28 17:10:10] Design: group comparison design (Different conditions contains different biological subjects).
#> INFO  [2023-02-28 17:10:10] Model fitting for 90 proteins.
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   2%
  |                                                                            
  |==                                                                    |   3%
  |                                                                            
  |===                                                                   |   4%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |=====                                                                 |   8%
  |                                                                            
  |======                                                                |   9%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |=========                                                             |  12%
  |                                                                            
  |=========                                                             |  13%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  16%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |============                                                          |  18%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  21%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |================                                                      |  23%
  |                                                                            
  |=================                                                     |  24%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |===================                                                   |  28%
  |                                                                            
  |====================                                                  |  29%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |======================                                                |  31%
  |                                                                            
  |=======================                                               |  32%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |=========================                                             |  36%
  |                                                                            
  |==========================                                            |  37%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |===========================                                           |  39%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |==============================                                        |  42%
  |                                                                            
  |==============================                                        |  43%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |=================================                                     |  48%
  |                                                                            
  |==================================                                    |  49%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================                                  |  51%
  |                                                                            
  |=====================================                                 |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |========================================                              |  57%
  |                                                                            
  |========================================                              |  58%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  61%
  |                                                                            
  |============================================                          |  62%
  |                                                                            
  |============================================                          |  63%
  |                                                                            
  |=============================================                         |  64%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |===============================================                       |  68%
  |                                                                            
  |================================================                      |  69%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |==================================================                    |  71%
  |                                                                            
  |===================================================                   |  72%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  76%
  |                                                                            
  |======================================================                |  77%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |=======================================================               |  79%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |==========================================================            |  82%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |===========================================================           |  84%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  87%
  |                                                                            
  |=============================================================         |  88%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |================================================================      |  91%
  |                                                                            
  |=================================================================     |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  96%
  |                                                                            
  |====================================================================  |  97%
  |                                                                            
  |====================================================================  |  98%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%
#> INFO  [2023-02-28 17:10:12] Testing for 90 proteins:
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   2%
  |                                                                            
  |==                                                                    |   3%
  |                                                                            
  |===                                                                   |   4%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |=====                                                                 |   8%
  |                                                                            
  |======                                                                |   9%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |=========                                                             |  12%
  |                                                                            
  |=========                                                             |  13%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  16%
  |                                                                            
  |============                                                          |  17%
  |                                                                            
  |============                                                          |  18%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  21%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |================                                                      |  23%
  |                                                                            
  |=================                                                     |  24%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |===================                                                   |  28%
  |                                                                            
  |====================                                                  |  29%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |======================                                                |  31%
  |                                                                            
  |=======================                                               |  32%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |=========================                                             |  36%
  |                                                                            
  |==========================                                            |  37%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |===========================                                           |  39%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |==============================                                        |  42%
  |                                                                            
  |==============================                                        |  43%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |=================================                                     |  48%
  |                                                                            
  |==================================                                    |  49%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================                                  |  51%
  |                                                                            
  |=====================================                                 |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |========================================                              |  57%
  |                                                                            
  |========================================                              |  58%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  61%
  |                                                                            
  |============================================                          |  62%
  |                                                                            
  |============================================                          |  63%
  |                                                                            
  |=============================================                         |  64%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |===============================================                       |  68%
  |                                                                            
  |================================================                      |  69%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |==================================================                    |  71%
  |                                                                            
  |===================================================                   |  72%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  76%
  |                                                                            
  |======================================================                |  77%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |=======================================================               |  79%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |==========================================================            |  82%
  |                                                                            
  |==========================================================            |  83%
  |                                                                            
  |===========================================================           |  84%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  87%
  |                                                                            
  |=============================================================         |  88%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |================================================================      |  91%
  |                                                                            
  |=================================================================     |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  96%
  |                                                                            
  |====================================================================  |  97%
  |                                                                            
  |====================================================================  |  98%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%
#> INFO  [2023-02-28 17:10:13] Design: 2 mixtures.
#> INFO  [2023-02-28 17:10:13] Design: 1 MS run per mixture.
#> INFO  [2023-02-28 17:10:13] Design: group comparison design (Different conditions contains different biological subjects).
#> INFO  [2023-02-28 17:10:13] Model fitting for 85 proteins.
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   2%
  |                                                                            
  |==                                                                    |   4%
  |                                                                            
  |===                                                                   |   5%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |======                                                                |   8%
  |                                                                            
  |=======                                                               |   9%
  |                                                                            
  |=======                                                               |  11%
  |                                                                            
  |========                                                              |  12%
  |                                                                            
  |=========                                                             |  13%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  15%
  |                                                                            
  |============                                                          |  16%
  |                                                                            
  |============                                                          |  18%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  21%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |================                                                      |  24%
  |                                                                            
  |=================                                                     |  25%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |====================                                                  |  28%
  |                                                                            
  |=====================                                                 |  29%
  |                                                                            
  |=====================                                                 |  31%
  |                                                                            
  |======================                                                |  32%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |=========================                                             |  35%
  |                                                                            
  |==========================                                            |  36%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |===========================                                           |  39%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |==============================                                        |  42%
  |                                                                            
  |==============================                                        |  44%
  |                                                                            
  |===============================                                       |  45%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |==================================                                    |  48%
  |                                                                            
  |===================================                                   |  49%
  |                                                                            
  |===================================                                   |  51%
  |                                                                            
  |====================================                                  |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |=======================================                               |  55%
  |                                                                            
  |========================================                              |  56%
  |                                                                            
  |========================================                              |  58%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  61%
  |                                                                            
  |============================================                          |  62%
  |                                                                            
  |============================================                          |  64%
  |                                                                            
  |=============================================                         |  65%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |================================================                      |  68%
  |                                                                            
  |=================================================                     |  69%
  |                                                                            
  |=================================================                     |  71%
  |                                                                            
  |==================================================                    |  72%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  75%
  |                                                                            
  |======================================================                |  76%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |=======================================================               |  79%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |==========================================================            |  82%
  |                                                                            
  |==========================================================            |  84%
  |                                                                            
  |===========================================================           |  85%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  87%
  |                                                                            
  |==============================================================        |  88%
  |                                                                            
  |===============================================================       |  89%
  |                                                                            
  |===============================================================       |  91%
  |                                                                            
  |================================================================      |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  95%
  |                                                                            
  |====================================================================  |  96%
  |                                                                            
  |====================================================================  |  98%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%
#> INFO  [2023-02-28 17:10:17] Testing for 85 proteins:
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   2%
  |                                                                            
  |==                                                                    |   4%
  |                                                                            
  |===                                                                   |   5%
  |                                                                            
  |====                                                                  |   6%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |======                                                                |   8%
  |                                                                            
  |=======                                                               |   9%
  |                                                                            
  |=======                                                               |  11%
  |                                                                            
  |========                                                              |  12%
  |                                                                            
  |=========                                                             |  13%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  15%
  |                                                                            
  |============                                                          |  16%
  |                                                                            
  |============                                                          |  18%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |===============                                                       |  21%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |================                                                      |  24%
  |                                                                            
  |=================                                                     |  25%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |====================                                                  |  28%
  |                                                                            
  |=====================                                                 |  29%
  |                                                                            
  |=====================                                                 |  31%
  |                                                                            
  |======================                                                |  32%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |=========================                                             |  35%
  |                                                                            
  |==========================                                            |  36%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |===========================                                           |  39%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |==============================                                        |  42%
  |                                                                            
  |==============================                                        |  44%
  |                                                                            
  |===============================                                       |  45%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |==================================                                    |  48%
  |                                                                            
  |===================================                                   |  49%
  |                                                                            
  |===================================                                   |  51%
  |                                                                            
  |====================================                                  |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |=======================================                               |  55%
  |                                                                            
  |========================================                              |  56%
  |                                                                            
  |========================================                              |  58%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  61%
  |                                                                            
  |============================================                          |  62%
  |                                                                            
  |============================================                          |  64%
  |                                                                            
  |=============================================                         |  65%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |================================================                      |  68%
  |                                                                            
  |=================================================                     |  69%
  |                                                                            
  |=================================================                     |  71%
  |                                                                            
  |==================================================                    |  72%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  75%
  |                                                                            
  |======================================================                |  76%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |=======================================================               |  79%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |==========================================================            |  82%
  |                                                                            
  |==========================================================            |  84%
  |                                                                            
  |===========================================================           |  85%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  87%
  |                                                                            
  |==============================================================        |  88%
  |                                                                            
  |===============================================================       |  89%
  |                                                                            
  |===============================================================       |  91%
  |                                                                            
  |================================================================      |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  94%
  |                                                                            
  |===================================================================   |  95%
  |                                                                            
  |====================================================================  |  96%
  |                                                                            
  |====================================================================  |  98%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%
head(MSstatsPTM.model$PTM.Model)
#>             Protein Label      log2FC         SE       DF       pvalue
#> 1: Protein_1076_Y67   1-4  0.11835636 0.05264970 15.00000 4.004178e-02
#> 2: Protein_1076_Y67   2-5  0.24162457 0.05264970 15.00000 3.544345e-04
#> 3: Protein_1076_Y67   3-6 -0.27968805 0.06173696 15.00028 3.984772e-04
#> 4: Protein_1076_Y67   1-3  0.42262536 0.05712141 15.00008 2.223242e-06
#> 5: Protein_1076_Y67   2-3  0.37549462 0.05712141 15.00008 8.829044e-06
#> 6: Protein_1076_Y67   4-6  0.02458095 0.05712141 15.00008 6.730757e-01
#>      adj.pvalue issue
#> 1: 0.0493665762    NA
#> 2: 0.0020224378    NA
#> 3: 0.0071725899    NA
#> 4: 0.0001000459    NA
#> 5: 0.0003973070    NA
#> 6: 0.7530134974    NA
head(MSstatsPTM.model$PROTEIN.Model)
#>         Protein Label    log2FC        SE DF      pvalue adj.pvalue issue
#> 1: Protein_1076   1-4 0.1511817 0.1459011  5 0.347602256 0.41614355    NA
#> 2: Protein_1076   2-5 0.3559027 0.1459011  5 0.058701203 0.09494067    NA
#> 3: Protein_1076   3-6 0.3195065 0.1786916  5 0.133803423 0.24198491    NA
#> 4: Protein_1076   1-3 0.4304476 0.1459011  5 0.031875419 0.07322731    NA
#> 5: Protein_1076   2-3 0.6261724 0.1459011  5 0.007776053 0.03478761    NA
#> 6: Protein_1076   4-6 0.5987725 0.1786916  5 0.020309479 0.05754353    NA
head(MSstatsPTM.model$ADJUSTED.Model)
#>              Protein Label      log2FC         SE     Tvalue        DF
#> 1:  Protein_1076_Y67   1-4 -0.03282532 0.15511001 -0.2116261  6.351078
#> 2: Protein_1145_T915   1-4 -1.26808260 0.24799278 -5.1133852 14.829339
#> 3: Protein_1146_S328   1-4  0.03359191 0.17861660  0.1880671 19.996633
#> 4: Protein_1160_S188   1-4 -0.24643910 0.14565603 -1.6919252 17.822868
#> 5:   Protein_12_S703   1-4 -0.24745688 0.10078246 -2.4553567 10.599996
#> 6: Protein_1220_Y321   1-4 -0.33005855 0.08668981 -3.8073512 24.562266
#>          pvalue  adj.pvalue GlobalProtein Adjusted
#> 1: 0.8390276607 0.868296067  Protein_1076     TRUE
#> 2: 0.0001318386 0.000879508  Protein_1145     TRUE
#> 3: 0.8527193852 0.872322130  Protein_1146     TRUE
#> 4: 0.1080693549 0.152669406  Protein_1160     TRUE
#> 5: 0.0326935599 0.054900506    Protein_12     TRUE
#> 6: 0.0008302273 0.003694511  Protein_1220     TRUE

1.3.1 Volcano Plot

The models from the groupComparisonPTM function can be used in the model visualization function, groupComparisonPlotsPTM. Here we show Volcano Plots for the models.

1.3.2 Heatmap Plot

Here we show a Heatmap for the models.