Prepare test data sets

[wolski]

Formats: raw, mzXML, mgf, dta, Rdata, DeisotoperJSON.

• Where do we store this data sets - r21 (CP)?
• We need peak picked data (no profile data).
• About 3 Hela data sets
  • in full size (approx 30.000 spectra)
  • an example subsets of about 10 spectra.
  • formats needed, raw, mgf, mzML (definitely an input working with MS-DConv).
• Finalize the MassSpectrumDTO and the MassSpectrometryMeasurementDTO

[cpanse]

Can we use that data here: http://fgcz-ms.uzh.ch/~cpanse/R257544/ ?

[cpanse]

• replace package mzXML file
• generated using msconvert GUI
• note, command line parameter don't seem to perform right

library(deisotoper)

mzXMLfilename <- system.file("extdata",
           name='20161010_04_TP_HeLa_200ng.mzXML', package = "deisotoper")
           
S <- as.psmSet.mzXML(openMSfile(mzXMLfilename))

plot(S[[1]]$mZ , S[[1]]$intensity, type='h', xlim=c(440,462))

[LucasSchmidt97]

We need more test data:

• mgf (or RData)
• This special cases/data, where Witold meant, that there would be much more isotopic clusters/isotopic sets and/or the scores should have more influence