Having trouble parsing latest Xcalibur 2.2 generated mzXML (q-executive) using Jrap

[David Zhao]

Hi there,

I'm having trouble parsing the latest Xcalibur 2.2 generated mzXML (q-executive) using Jrap: for some scans, scan.getMassIntensityList method returns negative float values for m/z and intensities.

Has anybody seen this before? I realized that we're using jrap-0.1.jar, just downloaded jrap-3.0.jar, but still getting negative values.

Thanks,

David