Re: [proteowizard-support] msconvert .wiff to mgf/mzML/mzXML

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

Hi Brett,

Your MGF had base64 in it? That sounds like some file or memory corruption. Were you writing to a 
network drive?

Current msconvert versions work fine with Triple TOF including peak picking (although depending on 
downstream analysis the peak picking might not be as good as with AB's own converter which uses a 
more aggressive Protein Pilot peak picker).

-Matt


On 7/19/2012 2:01 AM, Brett Chapman wrote:
> Hi
>
> I'm currently having problems running msconvert.
>
> I have some .wiff files from a Triple TOF 5600 (AB Sciex), and have converted to mzML, mzXML as well
> as MGF.
>
> When searching these files against MS/MS search tools like Mascot or Inspect I get numerous errors,
> using all different formats.
>
> The MGF file appears to have weird formatted regions the same as the long binary strings found in
> the mzXML or mzML files, at a number of random locations throughout the MGF file.
>
> I came across this post in the spctools discussion group
> (http://www.mail-archive.com/spc...@go.../msg03363.html), which stated that
> msconvert has issues with conversion of TripleTOF wiff files to MGF. This was posted last year. Is
> it still the case, that msconvert is unable to process Triple TOF wiff files?
>
> Cheers
>
> Brett