Re: [proteowizard-support] Question regarding msconvert.exe

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

  Hi Hua,

The T2D converter is pretty finicky and the least tested of our converters, so I'll cross my fingers and hope it works for you. A peak picking filter for all ms 
levels can be applied like:
msconvert data.t2d --filter "peakPicking true 1-"

For t2d data, you probably want to combine multiple t2ds into a single output file, so you'll probably want to pass the parent directory of a bunch of t2ds 
instead of a single t2d.

For example, if you have files:
runId/1.t2d
runId/2.t2d
runId/3.t2d

and you run:
msconvert runId --filter "peakPicking true 1-"

That will give you a single file with all 3 t2ds named "runId.mzML" (or MGF).

-Matt


On 7/19/2010 1:21 PM, Hua Xu wrote:
> Dear Sir/Madam,
>
> I am trying to incorporate ProteoWizard into our work flow for data conversion, 'cause it seems very powerful and generic. However, after reading the help 
> message from msconvert.exe carefully, I am still not sure about how to convert a Q-TOF MS/MS data file (t2d) to a MGF file with the spectrum CENTROIDED. Since 
> the MS/MS spectrum from Q-TOF has high mass accuracy, the default spectrum is of profile format. However, we need centroided MGF for database searches.
>
> Thanks,
>
> Hua