Precursor ion charge in blast_output.txt sometimes missing

[Thys Potgieter]

Hi Guys,

Please can you advise me how to interpret the charge when the charge field is blank in the blast_output.txt file ( I am using DeNovoGUI 1.13.1). I am trying to calculate precursor ion MW from mz and charge.

Here is an example, the first record has a charge but in the second record the charge field is empty.

>0843_198_23v2_rpt.mgf;0843_198_23v2_rpt.19381.19381.2 File:"0843_198_23v2_rpt.raw", NativeID:"controllerType=0 controllerNumber=1 scan=19381";568.327857611355;2+;;0.262581

IGAG

>0843_198_23v2_rpt.mgf;0843_198_23v2_rpt.5149.5149. File:"0843_198_23v2_rpt.raw", NativeID:"controllerType=0 controllerNumber=1 scan=5149";376.878875732422;;;0.00847334

GGDG

Can I assume the charge in such cases is 1+?

Thank you in advance for your assistance! 

Kind regards

Thys

[Harald Barsnes]

Hi Thys,

The charge in the header line in the BLAST export is the charge from the mgf file. In other words, if the charge is missing in the BLAST export it means that it was not annotated in the mgf file. Assuming that this charge is 1+ would therefore be incorrect.

I would recommend using the export Tag Matches option instead, as this one should contain all the information you need?

Best regards,

Harald

[Thys Potgieter]

Thank you Harald! I use Tag Match option instead.