Clarification on acquisitionNum vs scanIndex

[stanstrup]

I couldn't find a description of the difference between acquisitionNum, scanIndex and a few other scan variables.

In my file spIdx, seqNum, acquisitionNum and spectrum all appear to be the same and is just the number of the scan in the order recorded disregarding that they are different scanEvents (another matter is that there seems to be no easy way to distinguish scanEvents).

In the code it looks like scanIndex equals spIdx...

The documentation doesn't make it clearer in my mind...

acquisitionNum integer(1): the index of acquisition of a spectrum during a MS run.
scanIndex integer(1): the index of a spectrum within a (raw) file.

Would it be possible to describe the differences more explicitly?

[sgibb]

This is indeed quite complicated and convoluted:

• spectrumID is a vendor specific field in the mzML file that contains some information about the run/spectrum, e.g.: controllerType=0 controllerNumber=1 scan=5281 file=2
• acquisitionNum is a more a less sanitize spectrum id generated from the spectrumID field by mzR: https://github.com/sneumann/mzR/blob/master/src/pwiz/data/msdata/MSData.cpp#L552-L580
• scanIndex is the mzR generated sequence number of the spectrum in the raw file (which doesn't have to be the same as the acquisitionNum)
• seqNum seems to be similar to scanIndex but an mzML field (@jorainer is that correct?)
• spIdx/spectrum: no idea

[lgatto]

Thanks @sgibb - you beat me to it.

This is probably something we should add in the documentation, in MSnbase and Spectra.

[lgatto]

I have added a short description of this to the Spectra and MSnExp man pages.