An infuriating quirk of the WIFF APIs I've used is they return profile data without flanking zero
points around the peaks. So if those aren't inserted during conversion, the profile will appear to
never reach 0. The fix requires either a hack of inserting a zero point essentially before or after
each non-zero point, or a better but harder fix of actually trying to figure out the sample rate at
each non-zero data point and extrapolating the x coordinate of the flanking zero point from there.
This is the case with both WIFF APIs I've used, I'm not sure if it also applies to the Analyst API
mzWiff uses. I seem to recall that at some point I had the latter approach implemented in msconvert,
but it's not there now so I probably took it out for performance reasons and meant to return to it
later.
-Matt
On 1/19/2011 3:16 PM, Karina Chmielewski wrote:
We’re having issues with missing datapoints after converting wiff files to
mzXML. After conversion
with mzwiff, the “baseline” (0 intensity) datapoints seem to be missing in the
mzXML and a new
“baseline” is created that corresponds to the intensity of the lowest peak in
the original wiff file.
For example, see screenshot of the wiff from MultiQuant (before conversion).
The lowest peak
intensity is ~50.
After conversion with mzWiff to mzXML the basline is shifted to ~50 and all peaks
with intensity <
50 are gone. Any idea what might be causing this?
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