Re: [proteowizard-support] from mzML to mzXML

[Matthew C. <mat...@va...>]

Hi Silvia,

I think this is the first I've seen of mzML export from an ABI TOF/TOF 
database. MzML requires information about the source file, so there has 
been some consternation about how this should work for sources which are 
actually databases or directories. Someone just posted yesterday on the 
PSI-dev list about writing mzML from databases, but the ABI folks never 
did (which is surprising since they did post the nativeID format they 
wanted for the TOF/TOF). Hopefully that's one of the reasons it's still 
considered in beta. :)

The TOF/TOF case is actually the one we considered while developing 
mzML. We never had a great solution for it, but IIRC the one we settled 
on was that TOF/TOF was typically exported to T2D files and therefore 
the T2D files would be the source files. That doesn't apply for direct 
export from the database though. The reason mzML requires the source 
file information is so that it can store a checksum (SHA-1 hash) of the 
file so that authenticity and integrity of the source file can be proven 
at a later point (i.e. Did this XML file come from this RAW file? Yes, 
the checksums match.). Now that direct export from databases is looking 
likely, we will have to address this in the PSI working group: it may 
require a minor mzML revision. I think we will want to keep the checksum 
mechanism, but we will negotiate with database exporters to come up with 
a reasonable way to do it. After all, databases must have ways to verify 
their data integrity just like files do.

In the mean time, you can work around this issue by either using the 
mzML, or manually changing the parentFile after conversion to mzXML. If 
you open the XML in Wordpad or a better text editor, change:
<parentFile fileName="AK159/CNR Project folder\LC MALDI\VSMC\LC Anionica 
cationica VSMC 80C 10Ottobre08"
to
<parentFile fileName="AK159/CNR Project fo\LC MALDI\VSMC\LC Anionica 
cationica VSMC 80C 10Ottobre08.raw"

I added the .raw extension and deleted the corresponding number of 
characters from the word "folder." The total number of characters needs 
to stay the same in order to preserve the index.

Thanks,
-Matt


Silvia Rocchiccioli wrote:
> I have an Applied Biosystems 4800 MALDI TOF TOF analyzer. I obtain 
> mzML from every LC run containing all MS and MSMS information about 
> the run.
> mzML is created with "mzML_Exporter" beta version from Sean Seymour 
> (ABI) http://www.psidev.info/index.php?q=node/257.
>
> I tried to use ProteoWizard to convert mzML to mzXML. While mzMl with 
> seems.exe works well, the converted mzXML doesn't work give me a 
> warning message:
>
> ---------------------------
>> Unhandled Exception
>> ---------------------------
>> System.Exception: 
>> [Serializer_mzXML::translate_parentFileExtensionToSourceFileType] 
>> unknown file extension for parentFile "LC Anionica cationica VSMC 80C 
>> 10Ottobre08"
>>    in pwiz.CLI.msdata.MSDataFile..ctor(String path)
>>    in seems.OpenDataSourceDialog.listView_ItemSelectionChanged(Object 
>> sender, ListViewItemSelectionChangedEventArgs e)
>>    in 
>> System.Windows.Forms.ListView.OnItemSelectionChanged(ListViewItemSelectionChangedEventArgs 
>> e)
>>    in System.Windows.Forms.ListView.WmReflectNotify(Message& m)
>>    in System.Windows.Forms.ListView.WndProc(Message& m)
>>    in 
>> System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
>>    in 
>> System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m)
>>    in System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 
>> msg, IntPtr wparam, IntPtr lparam)
>> ---------------------------
>> OK  ---------------------------
>
> could you check my mzML format?....you find attached.
> Thank you
> Silvia