Problem with MGF import - object: mz values have to be sorted increasingly

[felipe-mansoldo]

Dear all,

I'm not able to import the GNPS .mgf obtained from: https://gnps-external.ucsd.edu/gnpslibrary download link: https://gnps-external.ucsd.edu/gnpslibrary/GNPS-LIBRARY.mgf

> mbank.gnps <- Spectra("GNPS-LIBRARY.mgf", source = MsBackendMgf() )
Start data import from 1 files ... done
Error in validObject(object) : 
  invalid class “MsBackendMgf” object: mz values have to be sorted increasingly

However, it is possible to import using MSnbase::readMgfData:

> mbank <- MSnbase::readMgfData("GNPS-LIBRARY.mgf", pdata = NULL, centroided = TRUE, smoothed = FALSE,
+                               verbose = TRUE, cache = 1)
Scanning GNPS-LIBRARY.mgf ...
  |===================================================================================================================| 100%
> length(mbank)
[1] 14190

I would like to import through Spectra to be able to use the package's functions. Is it possible to fix this? or convert MSnExp to Spectra?

Ideally it would be better to import through Spectra so we can keep the MGF information like SMILES, INCHI, NAME etc.

thanks

[jorainer]

Which version of Spectra and MsBackendMgf are you using?

[jorainer]

I can read the file without problems using the current stable version (for R 4.3, Bioconductor release 3.18). According to the NEWS a version > 1.7.4 would be needed.

[felipe-mansoldo]

Dear @jorainer It's true, it's an old version problem. I updated and everything is working perfectly, thanks!