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Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html
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AC$CHROMATOGRAPHY: SOLVENT C entry needed #176

Open schymane opened 7 years ago

schymane commented 7 years ago

We can only deal with two solvents (A and B) in settings, additional solvents have to be added post record generation. Need to expand settings to deal with this ... (I've just come across this again and have the workaround, posting this now so we don't forget it...). @meowcat should we just restrict to "solvent C" or deal with as many entries as necessary? Are there any realistic cases we'd expect with >3?

schymane commented 7 years ago

The hacked fix is here: https://github.com/MassBank/MassBankAdministrationScripts/blob/master/R%20projects/MBrecordToFile/addInfoToRecord.R e.g.

lc_settings <- c("87/13/0 at 0 min, 7/93/0 at 20 min, 0/0/100 at 20.2-26 min, 87/13/0 at 26.2 min, 87/13/0 at 32.3 min", "300 uL/min", "XBridge C18 3.5 um, 2.1x50 mm, Waters with guard column", "water with 0.1% formic acid", "methanol with 0.1% formic acid","isopropanol") changeRecordLCSettings("E:/UchemSpectra/Processed/AndreaTPs_AZ/merged_2302",lc_settings)

tsufz commented 7 years ago

So far, MB cannot handle a third entry. Needs to be fixed in the DB issues #_9 in MassBank-web. @Treutler @naperone

tsufz commented 7 years ago

We have also those cases, because we use a third solvent to clean the columns properly. A case >3 is not used (so far). But if the DB model is easily extendible, it should be no problem to add new tags in future.

sneumann commented 7 years ago

Hi @tsufz , can you point to where MB can't handle a third one ? The docs don't say AC$CHROMATOGRAPHY: SOLVENT C is forbidden.

2.4.6 Subtag: SOLVENT
Chemical Composition of Buffer Solution.  Iterative
Example
AC$CHROMATOGRAPHY: SOLVENT A acetonitrile-methanol-water (19:19:2) with 0.1% acetic acid
AC$CHROMATOGRAPHY: SOLVENT B 2-propanol with 0.1% acetic acid and 0.1% ammonium
schymane commented 7 years ago

The reason I first flagged this as an issue was because RMassBank didn't handle it as a setting, I am not aware of any restriction on the MassBank side and in fact have uploaded spectra with these three solvent entries in Eawag additional ... unless I am mistaken?

From: sneumann [notifications@github.com] Sent: Sunday, 13 August 2017 1:59 PM To: MassBank/RMassBank Cc: Schymanski, Emma; Author Subject: Re: [MassBank/RMassBank] AC$CHROMATOGRAPHY: SOLVENT C entry needed (#176)

Hi @tsufzhttps://github.com/tsufz , can you point to where MB can't handle a third one ? The docs don't say AC$CHROMATOGRAPHY: SOLVENT C is forbidden.

2.4.6 Subtag: SOLVENT Chemical Composition of Buffer Solution. Iterative Example AC$CHROMATOGRAPHY: SOLVENT A acetonitrile-methanol-water (19:19:2) with 0.1% acetic acid AC$CHROMATOGRAPHY: SOLVENT B 2-propanol with 0.1% acetic acid and 0.1% ammonium

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/MassBank/RMassBank/issues/176#issuecomment-322037853, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AD4a_VrrG8MGBKoXbe3wHERcDzI7bVU-ks5sXuUqgaJpZM4MJp1P.

meowcat commented 7 years ago

In RMassBank, IMO we should just change the settings from lc_solvent_a and lc_solvent_b to lc_solvent and make a named list for as many solvents as anyone wants to use. It's permitted in YAML if i'm not brutally mistaken.

tsufz commented 6 years ago

The 2.4.6 Subtag: SOLVENT specification has no restrictions on the number of solvents. It is iterative.