[M-2H]2- Adduct bug

[lauperbe]

I came across a bug for Spectra of Adducts [M-2H]2-.
MWE is attached.

The compound with ID 4339 has the formula: C8H4Cl2N2O7S2
The [M-2H]2- ion has a monoisotopic mass of 185.934572, which can be clearly seen in the raw file.

The error occurs during the msmsRead() function. The based on the list here:

RMassBank/R/leCsvAccess.R

Line 359 in 1d078a8

getAdductInformation <- function(formula){

mode="m2H_c2" should be what is needed for the [M-2H]2- Adduct.

during the msmsRead() function the error "assignment of an object of class “NULL” is not valid for @‘polarity’ in an object of class “Spectrum1”; is(value, "integer") is not TRUE" occurs.

Additionally the warning "In findMsMsHR.mass(msRaw, mz, mzCoarse, limit.fine, rtLimits, confirmMode + :
No precursor was detected for compound, 4339 with m/z 371.869144923819. Please check the mass and retention time window." appears.
The m/z 371.8691 is the m/z of the [M-2H]- ion, indicating that due to the error above it assumes a charge state of 1.

Thank you in advance
Benedikt

MWE including .mzXML files can be found here since they are too big for upload:
https://polybox.ethz.ch/index.php/s/VTpjPDD43KAjbHU
MWE_M2H.zip

[sneumann]

Kudos for providing the MWE! The ZIP is missing 202101_023_4339_ChlorothalonilTPR419492.mzXML,
could you upload that as well somewhere ? Yours, Steffen

[lauperbe]

The mzXML file are in the polyboxlink since they are to big to be directly uploaded.
https://polybox.ethz.ch/index.php/s/VTpjPDD43KAjbHU

[sneumann]

Darn, hadn't realised that was two separate links and hit the wrong one :-(
I can confirm the error class “NULL” is not valid for @‘polarity’
and the warning No precursor was detected for compound ...
on RMassBank_2.99.4 and 3.1.0. Yours, Steffen

[meowcat]

I have a parser that builds all data required for mz calculation directly from arbitrary adduct strings, and handles multiple charges correctly.

https://gist.github.com/meowcat/1df7c1b10002029d39bc2b8fd70e0b18

Should we eventually move to this? The only thing we still would need are a map from mode to adductString. We could think about dropping the "mode" and only using adductstrings directly, but having a non-special-character descriptor is not so bad for e.g. building filenames. Perhaps the "mode" could also be derived automatically? Or it can have a few standard values and the other are user-defined?

Note that this requires tidyverse packages. This would add a few dependencies but also allow to rewrite some code in leMsMs.R that currently awkwardly does what dplyr would easily do.

Note: doubly-charged fragments are not handled correctly by analyzeFormula for now, I think!