Additional peaksData columns?

[jorainer]

Looking at the code of peaksData,MsBackendRawFileReader it looks like you can extract more than just m/z and intensity values from the raw data files. Is that correct?

[cpanse]

@jorainer yes; the plan is using rawrr::readTrailer

https://github.com/fgcz/rawrr/blob/1b0ac1c5e79574fdcb75df63bab7b41f8291d8a0/R/rawrr.R#L1434

with that, any trailer information can be retrieved.

it just has to be implemented.

[jorainer]

Note that we have added an additional parameter columns to the peaksData method (https://github.com/rformassspectrometry/Spectra/blob/master/R/MsBackend.R#L735-L738). This would the user to define which columns/data to retrieve for peaks. The default is c("mz", "intensity") but, depending on the backend, also others could now be supported. As a result a numeric matrix with the additional columns would be returned.

The peaksVariables method (https://github.com/rformassspectrometry/Spectra/blob/master/R/MsBackend.R#L742-L745) would allow to show the supported columns to the user. The MsBackendTimsTOF already uses this (https://github.com/rformassspectrometry/MsBackendTimsTof/blob/main/R/MsBackendTimsTof.R#L181-L196).

[cpanse]

@jorainer #19 seems to be a start. whatsoever here, we use, of course, Spectra::spectraVariables. Possible columns for peaksData could be charge and resolution as displayed in Figure 1.