Questions about understanding the results

[Wang-kaifei]

Hi,

Recently, I ran MS-GF+ and got the .mzid result and converted it to .tsv format. In the 'protein' column, there is only one protein in each row. I would like to ask how to get the sameset of this protein?

Best, --Kaifei Wang

[alchemistmatt]

You should use the MzidToTsvConverter to convert .mzid files to .tsv. Download a .zip file with the program from here:

• https://github.com/PNNL-Comp-Mass-Spec/Mzid-To-Tsv-Converter/releases

When converting, you have three options, illustrated in batch file Convert_mzid.bat

• Option 1: do not unroll proteins: only the first protein for each PSM will be shown
  • This is the default behavior
  • For example output, see row 51 in file QC_Mam_19_01_1a_25Feb21_Rage_Rep-21-01-02_msgfplus_excerpt.tsv
• Option 2: unroll proteins: for PSMs with multiple proteins, write one line per protein
  • Use -unroll to instruct the program to do this
  • For example output, see rows 51, 52, and 53 in file QC_Mam_19_01_1a_25Feb21_Rage_Rep-21-01-02_unrolled_msgfplus_excerpt.tsv
  • Rows 51, 52, and 53 are nearly identical; the only thing that changes is the protein name
• Option 3: for PSMs with multiple proteins, combine protein names into a comma separated list
  • Use -proteinList to do this
  • For example output, see row 51 in file QC_Mam_19_01_1a_25Feb21_Rage_Rep-21-01-02_delimited_msgfplus_excerpt.tsv
  • Row 51 has TBB4A_MOUSE, TBB4B_MOUSE, TBB5_MOUSE

[Wang-kaifei]

I am surprised that you provide this feature soon ! ! ! The updated version is very easy to use, thank you very much for your help.