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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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msconvert (as part of OpenMS) --simAsSpectra --srmAsSpectra options wrong output for wiff files #2080

Open sbolushevsky opened 2 years ago

sbolushevsky commented 2 years ago

Hi,

I use msconvert as a part of the OpenMS package and noticed that when I use --simAsSpectra and/or --srmAsSpectra options for command line tool, spectra output are different than the ones that msconvertGUI generates (please find print screens for comparison attached).

I could not figure out what version of msconvert OpenMS uses but wanted to double check with you if the latest version has the same issue. Thank you.

N.B. TICs seem to look different as well.

msconvert_command_line_tool_output msconvertGUI_output

chambm commented 2 years ago

The mzML should have the version of pwiz used to create the file pretty close to the top of the file. Can you tell me what versions you compared?