Re: [proteowizard-support] wiff ->centroided mzXML

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

Hi Salvo,

I recommend using MSDataConverter with the -proteinpilot option and mzML output. Then you can use 
msconvert to go from mzML to mzXML if you need to.  You said you tried this, and the mzML contained 
no peaks. You didn't say whether you used -centroid or -proteinpilot. If you see no peaks with 
-proteinpilot, there is probably something wrong with the data (is it peptides?). Pwiz is not a good 
choice at the moment for peak picking on WIFF data.

-Matt


On 2/21/2012 12:50 PM, Cappadona, S. wrote:
> Dear Support,
>
> Can you suggest me the best option to create a */_centroided mzXML_/* from a TT5600 wiff file?
>
> I have been struggling with this problem for quite some time, and I had given up.
>
> But now I see that new releases of msconvert and MS_Data_Converter are out, so I would give it a new
> try.
>
> I have tried many options and combinations, but without success.
>
> -I thought I could use ABSciex MS_Data_Converter to create an mzML file, followed by mscoverter to
> create an mzXML. But centroided mzML from MS_Data_Converter look ‘almost’ empty (no peak information)
>
> -I see that I can also create mzML files with the option –profile or –proteinpilot.
>
> -Do you think I can then convert them by your msconvert? shal I use the peakpicking option? And
> prefer vendor algorithm? (I think ABSciex explicitly state that centroiding has problem, in the
> MS-Data_Converter manual)
>
> -Shall I better use msconvert straight away from wiff files?
>
> I mady many trial, with different operating systems, with vendor software installed or not …
>
> I already made new trials, but I still have many combinations to test …
>
> So I would really appreciate if you (or someone which I didn’t find in your mailing list) have
> already worked out a solution to my problem.
>
> Thanks a lot,
>
> Salvo