[proteowizard-support] wiff ->centroided mzXML

[Cappadona, S. <S.C...@uu...>]

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






Salvatore Cappadona, PhD
Hecklab - Biomolecular Mass Spectrometry and Proteomics Group - Bioinformatics | Utrecht University
H.R. Kruytbuilding | Padualaan 8 | room O.609 |3584 CH, Utrecht | The Netherlands
T. +31 (0)30 - 253 6149 | F. +31 (0)30 - 253 6919 | S.C...@uu...<mailto:S.C...@uu...>