Re: [proteowizard-support] Sciex Data: Vendor Peak Picking Algorithm Problems

[Chambers, M. <mat...@gm...>]

Hi Thomas,

I'm not able to reproduce this. Do your settings look like:


Thanks,
-Matt


On 3/11/2019 7:04 AM, Thomas Stricker wrote:
>
> Dear Proteowizard team,
>
>
> I've just converted my SWATH data (Wiff, Sciex) to mzXML with the latest version of msConvert and realised that the peak picking algorithm 
> was not doing it's job properly.
>
> I followed the guidlines and put the peak picking as the first filter in the list of added filters, then I added a filter to remove MS2 
> data (2nd position).
>
> I discovered this while using xcms-Camera, which told me that my data where probably not centroided.
>
>
> Please find attached a powerpoint document showing you the problem.
>
>
> Figure1(top): raw data, centroided in PeakView
>
> Figure2: converted data with msConvert, centroided in PeakView
>
> Figure3: converted data with msConvert, centroided in MsConvert with peak picking set to Vendors
>
> Figure4(bottom): converted data with msConvert, centroided in MsConvert with peack picking set to pwiz
>
>
> Am I missing something? Do I do something wrong?
>
>
> Thank you in advance!
>
>
> *Thomas Stricker*, Ph.D. Student
>