The simplest way to get what you want is to convert to MGF instead of mz[X]ML. You lose some
metadata that way, but you can keep both the mzML and the MGF and have the "best" of both worlds. I
highly recommend mzML instead of mzXML for WIFF data because it preserves the cycle and experiment
instead of turning them into an arbitrary "scan" number.
-Matt
On 1/20/2011 10:22 AM, bobxiong wrote:
Hi Matt,
I tried both SeeMS and Insilicos Viewer and I could see the spectra
for individual scans. However, there was no export feature for
exporting the peaks' data (mz and intensity) for the scans. What I'm
trying to accomplish here is to get a peak list (all peaks rather than
the base peak alone) for all the scans for a downstream manipulation.
To that end, I wonder msconvert can be configured to report the peak
element as numeric data instead of base64 encoded strimg. I gather
this is doable because msconvert already does it for the base peak
(basePeakMz and basePeakIntensity).
Thanks,
Bob
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