from mzML to mzXML

[Silvia]

I have an Applied Biosystems 4800 MALDI TOF TOF and I use an LC-MALDI
workflow. Applied Biosystems gave me a tool to convert all T2D files
from an LC-run in a mzML file. For every run I have one mzML
containing MS and MSMS information. The question is: Can I go back
from mzML to mzXML? The majority of software up to today uses mzXML
and not mzML format. If I try to convert directly from T2D to mzXML I
am not able to obtain all T2D files in only one mzXML, but I obtain
for every T2D one mzXML (for example with "convertpeaklist")
Thank you

[Matthew Chambers]

Hi Silvia,

It's easy to convert from mzML to mzXML with msconvert:
http://proteowizard.sourceforge.net/technical/formats/index.html

http://proteowizard.sourceforge.net/download.html

-Matt

[Silvia Rocchiccioli]

Hi Matt,
thank you.
I have tried to use ProteoWizard......., I can create the mzXML file
starting from mzML but when I try to open it with "seems.exe" a warning
message appears......
You find it attached.
Silvia

--

---------------------------------------

Silvia Rocchiccioli, PhD
Istituto di Fisiologia Clinica-CNR
Via Moruzzi 1
56124, Pisa

Tel: 050 315 3312
email:silvia.ro...@ifc.cnr.it

---------------------------------------

[Matt Chambers]

Try a later release of pwiz. I know that's the one that the web page
points to as the default, we're working on a way to improve that.

[Silvia Rocchiccioli]

Hi,
I tried the latest version:
pwiz-bin-windows-x86-vc90-1_6_1386.............but the error message is
the same:
---------------------------
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 the problem be related to our mzML?.....but when I try to open it
with seems.exe it works correctly.
Silvia

[Matthew Chambers]

Yes it appears to be something unexpected with your mzML. I tested it
myself just now with 1386 from Thermo RAW -> mzML -> mzXML and it
worked. Where'd the mzML come from? Let's move this to the pwiz-support
list.

-Matt