Hi,
I'm experiencing very long processing times for
ASAPRatioProteinRatioParser. On a large dataset (48 x 2 hr QTOF runs,
~100K spectrum IDs) ASAPRatioPeptideRatioParser completes within a
couple of hours, but ASAPRatioProteinRatioParser is taking days. I
assumed that the the peptide quantitation would be the slower step due
to chromatogram extraction from the mzXML, with the protein ratio
creation only involving rolling these ratios up to the protein level,
but this appears not to be the case.
Just wondering whether the large disparity in run-time between the
PeptideRatio and ProteinRatio parsers is expected?
Thanks,
DT
--
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford
Mon-Thu: CCMP, Roosevelt Drive
Tel: (+44) (01865 2)87784
Friday : Dunn School of Pathology, S. Parks Rd.
Tel: (+44) (01865 2)75557
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