Re: [proteowizard-support] msconvert and PIS / MPIS data from Thermo and Sciex

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

Hi Ronny,

Did you try mzML? Precursor ion scans have productMZ instead of precursorMZ and mzXML doesn't 
support that. We could misuse the precursorMZ element, but I don't want to go there.

-Matt


On 10/19/2011 3:58 AM, Ronny Herzog wrote:
> Dear Matt,
>
> I wanted to switch from ReAdW.exe and mzWiff.exe to msconvert now, but I encountered some problems.
>
> 1) Conversion of multiple precursor ion scan (MPIS) data from *.wiff to *.mzXML worked with the new
> version of Analyst. However, it did not store the fragment masses for the PIS spectra. Without, the
> spectra are meaningless. Is there a way to extract this? (I created the tag <precursorMz>, but left
> it empty. This made my mzXML reader crashing)
>
> 2) Conversion of PIS *.raw files had the same problems. If I would do it with ReAdW.exe, I would
> read the fragment masses from the filterLine. Is there a way to include the filter line into the
> converted *.mzXML's?
>
> Thank you for your help,
> Ronny