text: user3061: 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 Following, these instructions` which seem terribly outdated.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
  
  
  user3848: 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
  
  user3913: Try this Docker container.
  All the vendor formats work except T2D, YEP, and FID.
  
original_text: 3061: <p>I am trying to run proteowizzard using wine to be able to convert raw mass spectrometry files to myML format. Following, <a href="http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine" rel="nofollow noreferrer">these instructions</a>` which seem terribly outdated. I am getting many issues. I am running Ubuntu 16.04.</p>
  
  <p>We want to convert output from a ThermoFisher instrument to mzML or mzXML format.</p>
  
  <pre><code>&gt; ~/software/proteowizzard&gt;wine msconvert.exe 
  &gt; fixme:heap:HeapSetInformation (nil) 1 (nil) 0
  &gt; fixme:heap:HeapSetInformation (nil) 1 (nil) 0
  &gt; fixme:process:SetProcessShutdownParameters (00000380, 00000000):
  &gt; partial stub. err:module:import_dll Library VCOMP110.DLL (which is
  &gt; needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\baf2sql_c.dll") not
  &gt; found err:module:import_dll Library baf2sql_c.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library MSVCP140.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library VCRUNTIME140.dll (which is needed
  &gt; by L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-runtime-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-heap-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-convert-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-stdio-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-string-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library
  &gt; api-ms-win-crt-environment-l1-1-0.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library
  &gt; api-ms-win-crt-filesystem-l1-1-0.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-time-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-locale-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-math-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library MSVCP140.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library VCRUNTIME140.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-runtime-l1-1-0.dll (which
  &gt; is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-string-l1-1-0.dll (which
  &gt; is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-stdio-l1-1-0.dll (which
  &gt; is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-filesystem-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-time-l1-1-0.dll (which is
  &gt; needed by L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll")
  &gt; not found err:module:import_dll Library
  &gt; api-ms-win-crt-convert-l1-1-0.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-environment-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-locale-l1-1-0.dll (which
  &gt; is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-heap-l1-1-0.dll (which is
  &gt; needed by L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll")
  &gt; not found err:module:import_dll Library api-ms-win-crt-math-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library api-ms-win-crt-utility-l1-1-0.dll (which
  &gt; is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msparser.dll") not found
  &gt; err:module:import_dll Library msparser.dll (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:import_dll Library api-ms-win-crt-utility-l1-1-0.dll
  &gt; (which is needed by
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe") not
  &gt; found err:module:LdrInitializeThunk Main exe initialization for
  &gt; L"Z:\\home\\swacker\\software\\proteowizzard\\msconvert.exe" failed,
  &gt; status c0000135
  </code></pre>
   3848: <p>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 <a href="https://www.playonmac.com/en/" rel="nofollow noreferrer">here</a></p>
   3913: <p>Try this Docker <a href="https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses" rel="nofollow noreferrer">container</a>.</p>
  
  <p>All the vendor formats work except T2D, YEP, and FID.</p>
  