MSConvert batch processing issue

[proteowizard]

MSConvert batch processing issue

[chambm]

Can you attach some screenshots demonstrating the problem? By "scan remain empty" do you mean an entire file, or just a few scans within the file?

[saersamani]

Please see two screenshots below. The first one shows the used parameters. and the second one shows the same files converted individually (folder called "mzXML_Files") and as a batch (folder called "Raw_Data_Pos"). As you can see the file "EA_001A" is completely empty in the batch mode and also the other files do not record all the scans.

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On 7/24/2019 5:09 PM, Matt Chambers wrote: Can you attach some screenshots demonstrating the problem? By "scan remain empty" do you mean an entire file, or just a few scans within the file? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#590?email_source=notifications&email_token=AHA45FBMTT7N55222QNMAJTQBBWCFA5CNFSM4IGPO7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2WUS7Q#issuecomment-514673022>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHA45FFSHUYBT5IM5YX25QLQBBWCFANCNFSM4IGPO7JQ>.

[chambm]

I think you'll need to visit the GitHub issue directly to post attachments. The screenshots didn't come through.

[saersamani]

Here are the screenshots.

[chambm]

The "note: the input only contains chromatogram data" message means you should use the "SIM as Spectra" and/or "SRM as Spectra" options. How were the files in the "mzXML" directory created?

[saersamani]

The first screenshot shows the parameter settings for the conversion. As you can see in that picture, none of those were checked. I will try again with “SIM as Spectra” and will let you know.

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On 26 Aug 2019, at 17:27, Matt Chambers ***@***.***> wrote: The "note: the input only contains chromatogram data" message means you should use the "SIM as Spectra" and/or "SRM as Spectra" options. How were the files in the "mzXML" directory created? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#590?email_source=notifications&email_token=AHA45FGEANF5AM5UZTCXQOLQGPY7DA5CNFSM4IGPO7J2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5EW66A#issuecomment-524906360>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHA45FCHNEVJABZURWPM3XTQGPY7DANCNFSM4IGPO7JQ>.

[saersamani]

Checking the SIM option solved the problem. Thanks for the help.

[sorenwacker]

How can I load multiple file in there? Like 100.... ok, got it.