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cbielow / PTXQC

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
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PTXQC v0.82.03 crashes with MaxQuant 1.2 input #33

Closed cbielow closed 7 years ago

cbielow commented 7 years ago

Reason: MaxQuant 1.2 uses 'BasePeak Intensity' as column name in msmsscans.txt, whereas MaxQuant 1.3+ use 'Base Peak Intensity'.

Workaround for affected PTXQC versions: set 

    enabled: no

in the .yaml file

the error message looks like this:

... MS^2*Scans: Ion Inj Time  done
Starting to work on MS^2*Scans: Intensity ...
Warning in .self$checkInput(c("fc.raw.file", "total.ion.current", "base.peak.intensity"),  :
  Input check failed: columns 'base.peak.intensity' are not present in input data!
 Show Traceback

 Rerun with Debug
 Error: .self$checkInput(c("fc.raw.file", "total.ion.current", "base.peak.intensity"),  .... is not TRUE
cbielow commented 7 years ago

fixed in PTXQC v0.82.04 (https://github.com/cbielow/PTXQC/commit/ac8ae14266a1f4d880fb94a194e57f913d34154f)