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sneumann / mzR-playground

Playground area for the mzR package. The main code repository is now at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR/
http://bioconductor.org/packages/devel/bioc/html/mzR.html
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Collision mode and polarity in header()? #16

Open meowcat opened 12 years ago

meowcat commented 12 years ago

Hi,

for some applications, it would be nice to have collision mode information (for MS2 spectra) and polarity information (for both MS1 and MS2 spectra in the header() output. The information is contained in both mzXML and mzML files made with ProteoWiz MSconvert GUI from ThermoScientific RAW files. I haven't tried other formats.

Polarity is in scan@polarity for mzXML and spectrum/cvParam@name = "positive scan" (or "negative scan") in mzML. Collision mode is in scan/precursorMz@activationMethod for mzXML, and in spectrum/precursorList/precursor/activation for mzML.