Body: <p>I have an .mzTab file, with PRT and PSM values.  Does anyone know of any specific functions that I could use to calculate protein abundance values from this data?</p>
  <p><strong>More details</strong></p>
  <p><a href="https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/1_0-Proteomics-Release/20minute_guide_mzTab.pdf" rel="nofollow noreferrer">This is a summary of what the mzTab file is.</a></p>
  <p>The data I have has two main sections within the file - a PRT section and a PSM section.</p>
  <p>The PRT section has protein information.  It has the following column headers:</p>
  <pre><code> [1] &quot;accession&quot;                        &quot;description&quot;                     
   [3] &quot;taxid&quot;                            &quot;species&quot;                         
   [5] &quot;database&quot;                         &quot;database_version&quot;                
   [7] &quot;search_engine&quot;                    &quot;best_search_engine_score[1]&quot;     
   [9] &quot;search_engine_score[1]_ms_run[1]&quot; &quot;num_psms_ms_run[1]&quot;  
  [11] &quot;modifications&quot;                   
  </code></pre>
  <p>Where <code>num_psms_ms_run</code> is the count of the total significant PSMs that can be mapped to the reported protein.</p>
  <p>The PSM section has peptide spectrum match information.  It has the following column headers:</p>
  <pre><code> [1] &quot;sequence&quot;                              
   [2] &quot;PSM_ID&quot;                                
   [3] &quot;accession&quot;                             
   [4] &quot;unique&quot;                                
   [5] &quot;database&quot;                              
   [6] &quot;database_version&quot;                      
   [7] &quot;search_engine&quot;                         
   [8] &quot;search_engine_score[1]&quot;                
   [9] &quot;search_engine_score[2]&quot;                
  [10] &quot;search_engine_score[3]&quot;                
  [11] &quot;modifications&quot;                         
  [12] &quot;retention_time&quot;                        
  [13] &quot;charge&quot;                                
  [14] &quot;exp_mass_to_charge&quot;                    
  [15] &quot;calc_mass_to_charge&quot;                   
  [16] &quot;spectra_ref&quot;                           
  [17] &quot;pre&quot;                                   
  [18] &quot;post&quot;                                  
  [19] &quot;start&quot;                                 
  [20] &quot;end&quot;                                   
  [21] &quot;opt_global_mzidentml_original_ID&quot;      
  [22] &quot;opt_global_cv_MS:1002217_decoy_peptide&quot;
  [23] &quot;opt_global_cv_PRIDE:0000091_rank&quot;     
  </code></pre>
  <p>More information about the column definitions <a href="http://psidev.info/sites/default/files/2017-07/v_1_0_0_mzTab_format_specification.pdf" rel="nofollow noreferrer">can be found here</a>.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-16T10:27:06.393Z
Comments.Text: Hi @icedcoffee please do supply more detail for example I'm not sure what the acronyms are, I'm pretty sure your question is fairly easy whether directly or indirectly by customised code.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-16T10:33:39.233Z
Comments.Text: Thank you, I've updated the question to include more information
Comments.UserDisplayName: icedcoffee
Tags: <proteomics>
Title: How to calculate protein abundance from an .mzTab file?
ThreadText: # How to calculate protein abundance from an .mzTab file?
  
  (Asked by: username_0 on 2020-12-16)
  
  I have an .mzTab file, with PRT and PSM values. Does anyone know of any specific functions that I could use to calculate protein abundance values from this data?
  
  **More details**
  
  [This is a summary of what the mzTab file is.](https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/1_0-Proteomics-Release/20minute_guide_mzTab.pdf)
  
  The data I have has two main sections within the file - a PRT section and a PSM section.
  
  The PRT section has protein information. It has the following column headers:
  
  ```
   [1] "accession"                        "description"                     
   [3] "taxid"                            "species"                         
   [5] "database"                         "database_version"                
   [7] "search_engine"                    "best_search_engine_score[1]"     
   [9] "search_engine_score[1]_ms_run[1]" "num_psms_ms_run[1]"  
  [11] "modifications"                   
  
  ```
  
  Where `num_psms_ms_run` is the count of the total significant PSMs that can be mapped to the reported protein.
  
  The PSM section has peptide spectrum match information. It has the following column headers:
  
  ```
   [1] "sequence"                              
   [2] "PSM_ID"                                
   [3] "accession"                             
   [4] "unique"                                
   [5] "database"                              
   [6] "database_version"                      
   [7] "search_engine"                         
   [8] "search_engine_score[1]"                
   [9] "search_engine_score[2]"                
  [10] "search_engine_score[3]"                
  [11] "modifications"                         
  [12] "retention_time"                        
  [13] "charge"                                
  [14] "exp_mass_to_charge"                    
  [15] "calc_mass_to_charge"                   
  [16] "spectra_ref"                           
  [17] "pre"                                   
  [18] "post"                                  
  [19] "start"                                 
  [20] "end"                                   
  [21] "opt_global_mzidentml_original_ID"      
  [22] "opt_global_cv_MS:1002217_decoy_peptide"
  [23] "opt_global_cv_PRIDE:0000091_rank"     
  
  ```
  
  More information about the column definitions [can be found here](http://psidev.info/sites/default/files/2017-07/v_1_0_0_mzTab_format_specification.pdf).
  
  **Tags:** proteomics
  
  > **Comments:**
  > **username_1**: Hi @username_0 please do supply more detail for example I'm not sure what the acronyms are, I'm pretty sure your question is fairly easy whether directly or indirectly by customised code.  
  > **username_0**: Thank you, I've updated the question to include more information  
  
  ---
  
  ## 0 answers
  
  