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I am trying to run proteowizzard using wine to be able to convert raw mass spectrometry files to myML format. Following, these instructions` which seem terribly outdated. I am getting many issues. I am running Ubuntu 16.04.

We want to convert output from a ThermoFisher instrument to mzML or mzXML format.

> ~/software/proteowizzard>wine msconvert.exe 
> fixme:heap:HeapSetInformation (nil) 1 (nil) 0
> fixme:heap:HeapSetInformation (nil) 1 (nil) 0
> fixme:process:SetProcessShutdownParameters (00000380, 00000000):
> partial stub. err:module:import_dll Library VCOMP110.DLL (which is
> needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\baf2sql_c.dll") not
> found err:module:import_dll Library baf2sql_c.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library MSVCP140.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library VCRUNTIME140.dll (which is needed
> by L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-runtime-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-heap-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-convert-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-stdio-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-string-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library
> api-ms-win-crt-environment-l1-1-0.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library
> api-ms-win-crt-filesystem-l1-1-0.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-time-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-locale-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-math-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library MSVCP140.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library VCRUNTIME140.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-runtime-l1-1-0.dll (which
> is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-string-l1-1-0.dll (which
> is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-stdio-l1-1-0.dll (which
> is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-filesystem-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-time-l1-1-0.dll (which is
> needed by L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll")
> not found err:module:import_dll Library
> api-ms-win-crt-convert-l1-1-0.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-environment-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-locale-l1-1-0.dll (which
> is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-heap-l1-1-0.dll (which is
> needed by L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll")
> not found err:module:import_dll Library api-ms-win-crt-math-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library api-ms-win-crt-utility-l1-1-0.dll (which
> is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
> err:module:import_dll Library msparser.dll (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:import_dll Library api-ms-win-crt-utility-l1-1-0.dll
> (which is needed by
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
> found err:module:LdrInitializeThunk Main exe initialization for
> L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe" failed,
> status c0000135
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  • $\begingroup$ Which issues did you find? You mention wine, so I assume you are using a linux computer to run a program for windows. Could you add more information about the requirements of this program? $\endgroup$
    – llrs
    Commented Sep 18, 2018 at 6:56
  • $\begingroup$ It might be better to ask this on Ask Ubuntu, but either way please edit and show us exactly what commands you ran and the specific errors you are getting. We can't help you if you don't tell us what the symptoms are. $\endgroup$
    – terdon
    Commented Sep 18, 2018 at 8:08
  • $\begingroup$ I am wondering whether there is anyone here who runs proteowizzard on linux, who knows how to set it up. $\endgroup$
    – Soerendip
    Commented Sep 18, 2018 at 17:01

2 Answers 2

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Try this Docker container.

All the vendor formats work except T2D, YEP, and FID.

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I sympathize ... If it is a Mac just run 'PlayonMac' its a brilliant frontend for Wine without all the bugs and hassles it causes. Its free and available here

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