[proteowizard-support] Enquiry about converting wiff file to mzML format using qtofpeakpicker

[Melody L. M. T. <man...@um...>]

Dear Sir/Madam,
Hello! I am new to the qtofpeakpicker tool in the ProteoWizard package.
When using msconvert, it is possible to specify the output file as MZML
format or MZXML format.
However, in the qtofpeakpicker page:

*qtofpeakpicker* is a command line tool for peak detection in TOF (Time Of
Flight spectra)

   - *Input:* same file formats as msconvert, explicitely those containing
   TOF raw data (wiff - AB-Sciex and Bruker baf files)
   - *Output:* same formats as msconvert (mzXML and mzML)

However,  I cannot find the argument for specifying the output as mzML. I
have tried to set the output as -O mywiff.mzML but it turns out to be a
MZXML file with the file extension as MZML.

Would you please give me some advice on how to convert wiff file to mzML
format using qtofpeakpicker?

Thank you very much!

Yours truly,

Melody Lam

--------------------------------------------
Melody M. T. Lam
B.Sc (Hons), PhD. (CUHK)
Proteomics Core, Faculty of Health Sciences,
University of Macau, China
Tel.: (853) 8822 2534/2526
E-mail: man...@um...
Website:
http://fhs.umac.mo/research/core-laboratories-and-facilities/proteomics-core/