how can I use the output data from Decontools

沙

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Nov 23, 2024, 3:06:29 AM11/23/24

to GlycReSoft

Dear sir or madam，

I found the article mentioned that Decontools processes data files and then imports them into Glycresoft, but I didn’t see the specific usage method. Could you please teach me how to use it?

Thanks.

Joshua Klein

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Nov 23, 2024, 12:48:24 PM11/23/24

to 沙, GlycReSoft

Hello,

The original GlycReSoft used DeconTools (or Decon2LS) for LC-MS deisotoping and charge state deconvolution. The DeconTools algorithm wasn't sensitive enough for some applications so in later versions we implemented our own deconvolution as part of the package. It is still a separate step that takes either an mzML file or, on Windows, a Thermo RAW file.

Thank you,

Joshua Klein

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Joshua Klein

沙

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Nov 25, 2024, 4:03:09 AM11/25/24

to GlycReSoft

Thanks for your reply.

According to your prompt, I imported my file converted by ms converte, and found an error, but it is normal to use the file the Project PXD003498 provided.

The error file is presented in .txt format. and the software is like the photo below. Are there some parameters going wrong or any other complications?

Hope you can help me to solve my confusion.

If necessary, I can afford my raw data for you. Thanks agian.

error.txt

Joshua Klein

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Nov 25, 2024, 10:35:35 AM11/25/24

to 沙, GlycReSoft

Hello,

Looking at that error message, I am afraid I will need to see your mzML file to understand what is going wrong. You can upload it and/or the raw file to https://www.dropbox.com/request/0sVSNOjXuBVSLqlgAjkk or provide sharing link through a platform of your choice.

Thank you,

Joshua Klein

To view this discussion visit https://groups.google.com/d/msgid/glycresoft/b402d7f3-68a5-409b-9b44-a3081c5541e2n%40googlegroups.com.

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Joshua Klein

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沙

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Nov 26, 2024, 1:46:05 AM11/26/24

to GlycReSoft

Thank you so much for your kind offer to help. I have uploaded the mzML file and the raw file to a website as you suggested.

I am appreciate you can help me.

Joshua Klein

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Nov 26, 2024, 9:47:03 AM11/26/24

to 沙, GlycReSoft

Thank you for sharing your files. It seems there are both mass spectra and electromagnetic radiation spectra in this file, and GlycReSoft doesn't know what to do with the EMR spectra. To fix this, please re-export your raw data using MSConvert with the following filter applied:

This should select only the mass spectra since the EMR spectra have an MS level of 0 as far as ProteoWizard is concerned.

Thank you,

Joshua Klein

To view this discussion visit https://groups.google.com/d/msgid/glycresoft/a33a3f62-c328-427c-a1ba-0ef3f165600fn%40googlegroups.com.