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ProteoWizard / pwiz

The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.
http://proteowizard.sourceforge.net/
Apache License 2.0
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Issue with demultiplexing Thermo Raw staggered windows #3175

Open ZeshanAlimq opened 1 day ago

ZeshanAlimq commented 1 day ago

Thanks for building this amazing platform.

I’m attempting to build a chromatogram library using gas-phase fractionation (GPF). I ran six DIA staggered GPFs covering the 400-1000 m/z range on the Thermo Eclipse. I attempted to demultiplex using MSConvert on Windows using the settings shown in the image. Msconvert setting up parrameters

I'm getting the following error. MsConvert error

Raw files and method files are available here (file://SCI-6682/Users/45774862/OneDrive%20-%20Macquarie%20University/BrainRAW) Thank you

nickshulman commented 1 day ago

The link where you say to download the files does not work. I think that URL only makes sense on your own computer. Maybe you could upload the files here: https://skyline.ms/files.url

ZeshanAlimq commented 1 day ago

Hi Nick, Thanks for the quick response. I have uploaded the files with the Zip name Zeshan.

nickshulman commented 1 day ago

Thank you for uploading those files. Your data does not seem to have any overlapping isolation windows. The isolation window for every spectrum is [519.76501-528.76501] You can use ProteoWizard SeeMS.exe to look at your data. image

The "unknown exception" that MSConvert is hitting is "integer divide by zero". We should probably fix MSConvert so that it gives a better error message in this case.

ZeshanAlimq commented 1 day ago

Thank you Nick for the help.