<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>

CC BY-SA 4.0
2019-01-02T15:09:05.303Z
2019-01-02T15:31:20.417Z
2019-01-02T15:31:20.417Z
Matt Chambers
<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>

CC BY-SA 4.0
2019-01-02T19:35:36.650Z
2019-01-02T19:35:36.650Z
M__
<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` which seem terribly outdated.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>

CC BY-SA 4.0
2018-09-18T06:56:28.183Z
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?
llrs
CC BY-SA 4.0
2018-09-18T08:08:30.523Z
It might be better to ask this on [ubuntu.se], 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.
terdon
CC BY-SA 4.0
2018-09-18T17:01:00.427Z
I am wondering whether there is anyone here who runs proteowizzard on linux, who knows how to set it up.
Soerendip
<mass-spectrometry>
How to run proteowizzard on linux using wine?
# How to run proteowizzard on linux using wine?

(Asked by: username_0 on 2018-09-17)

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

**Tags:** mass-spectrometry
> **Comments:**
> **username_1**: 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?  
> **username_2**: It might be better to ask this on [ubuntu.se], 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.  
> **username_0**: I am wondering whether there is anyone here who runs proteowizzard on linux, who knows how to set it up.  

---

## 2 answers

### Answer by username_3 on 2019-01-02. Score: 3 | Accepted answer

Try this Docker [container](https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses).

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


---

### Answer by username_4 on 2019-01-02. Score: 1

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](https://www.playonmac.com/en/)


---

