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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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Precursor data is not available for mzData files #7

Closed lgatto closed 13 years ago

lgatto commented 13 years ago

Using the pride experiment 12011 as an example, precursor data (charge, intensity, ...) are not available:

f [1] "/home/lgatto/Data/PRIDE_Exp_mzData_Ac_12011.xml" mzd <- openMSfile(f) 3: >/home/lgatto/Data/PRIDE_Exp_mzData_Ac_12011.xml hd <- header(mzd) head(hd[hd$msLevel>1,c(3,7,8,9,13,14,15,16)]) msLevel basePeakMZ basePeakIntensity collisionEnergy precursorScanNum 1 2 0 0 0 0 2 2 0 0 0 0 3 2 0 0 0 0 4 2 0 0 0 0 5 2 0 0 0 0 6 2 0 0 0 0 precursorMZ precursorCharge precursorIntensity 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0

I don't have another mzdata file with MS2 spectra at hand right now to double check.

lgatto commented 13 years ago

This issue is not fixed. I think that this is an issue with the ramp code and it is probably better not to invest too much time in this but rather get it working for the pwiz code. Anyway, I would expect most users to have mzXML or mzML.