Question: How to calculate protein abundance from an .mzTab file?
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10 weeks ago by
psyc_biostars0 wrote:

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?'

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.

proteomics • 148 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by psyc_biostars0
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