Molecular Networking Errors/ Conversion of .d files to MzXML using Proteowizard

[OLADIPUPO AKOLADE]

Hi GNPS community,

I am using .d raw files from Agilent LCMS. I used Proteowizard to convert it to
.mzXML for GNPS molecular networking, however, during analysis, this is the
message that shows:

ERROR: convert2.cpp : 145: Error loading file: inputspectra/spec-00000.mzXML
ERROR: ExecMergeConvert.cpp : 147: convert exited in error for file:
inputspectra/spec-00000.mzXML
ERROR: main_specnets.cpp : 244: Input spectra set is empty for file
inputspectra/spec-00000.mzXML
ERROR: main_specnets.cpp : 262: Input spectra set is empty
ERROR: main_specnets.cpp : 263: Please make sure input files are
32-bit uncompressed mzXML files that contain MS/MS spectra
ERROR: main_specnets.cpp : 949: Failed loading initial data.
Tool execution terminates abnormally with exit code [1]

Could you please assist me on this matter.

What are the parameters on Proteowizard for converting .d Agilent
files to MzXML for GNPS?

Your reply is highly appreciated.

Akolade

[Biswapriya Biswavas Misra]

Hi Akolade,

Here is a screenshot for the MSConvert settings (yellow highlighted are specific ones) that I use for Agilent  .D raw file conversion to .mzXML or .mzML and should work fine!

Please also check if at the acquisition stage the instrument was set in a way to acquire MS/MS data or not- many times that is the case.

Thanks,

Biswa

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[OLADIPUPO AKOLADE]

Hi Biswa,

Thank you for the MSConvert parameters. It worked. I was able to
convert Agilent .D raw files to .mzXML. And the resulting file worked
fine on GNPS.

Thanks and regards.
Akolade

[Felippe Dalpiaz]

Hello Biswapriya,

I'm very thankful for your contribution.

I'm facing the same issue that my colleague OLADIPUPO presented. So, I looked at your suggestion for him and followed suit.

The Peak Picking looks the same as yours, with the ms level at 1-2. However, when I try to add the Subset, I click on "Add," but nothing happens. It seems like it doesn't want to add the Subset option to the Filter. OLADIPUPO seemingly managed to do it, so it doesn't appear to be an issue with MSConvert.

Do you have any recommendations for me to achieve this? Could it be a problem with the output data from my Agilent instrument?

Thank you very much.