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MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html
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Precursor mz/rt search in raw data #201

Open Treutler opened 6 years ago

Treutler commented 6 years ago

I observed that there is a code branch which completely ignores the precursor m/z while searching for the right MS/MS spectrum: https://github.com/MassBank/RMassBank/blob/master/R/leMsmsRaw.R#L512

Is this intended in case the wrong adduct was specified? However, this can lead to wrongly selected MS/MS spectra which are treated and exported as usual. I have the feeling that this is dangerous.

Any opinions?

schymane commented 6 years ago

If I recall correctly we had to have a workaround for cases where MS1 and MS2 are in separate files (happens on some instruments), so the MS2 to access is guided differently. Should only be used in the correct context. May also be useful to deal with DIA data where the precursor is not exact. Please don’t remove any of these special options … there is a reason for most things Michele did :-)

Treutler commented 6 years ago

Maybe the best way to deal with this is to add the optional option to prevent this. At least in my case I observe that this leads to the selection of completely wrong MS/MS spectra without any warning and I only noticed it because I am working on more verbose console messages.

meowcat commented 6 years ago

@schymane: I didn't do it, that was Erik, it's the XCMS workflow :)

schymane commented 6 years ago

Ahha sorry @meowcat I didn’t click the link. Would indeed be good if additional checks are added to the xcms workflow if needed to avoid bad results. I misunderstood and thought it may have been the Bruker (?) workaround … I have little experience with the xcms workflow.