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

[Thomas S. <Tho...@un...>]

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
University of Geneva
Life Sciences Mass Spectrometry
Department of Inorganic and Analytical Chemistry
24, quai Ernest-Ansermet, 1211 Genève 4

E-mail: Tho...@un...
Phone: +41 22 379 33 10