NILU new spectra edited

[JeanFromentNILU]

No description provided.

[sneumann]

Hi, thanks for the new batch !
Rene is the authoritative source, but let me give some quick quesses from my side.

• 32 records end with double-slash and an empty line, instead they should end with the last peak

//

The CH$SMILES expected means that the CH$ section is missing the SMILES (and InChI in case of NILU-NL0136 I checked)
AC$MASS_SPECTROMETRY: MS_TYPE MS1 should be just AC$MASS_SPECTROMETRY: MS_TYPE MS
Several files are lacking the AC$INSTRUMENT_TYPE: LC-ESI-QFT
Regarding the SPLASH in NILU-NL0134 we'd need to check if that is an inconsistency in the way they are calculated. Which SPLASH Implementation/Language are you using ?
Not flagged by the validation, but you have double space in AC$INSTRUMENT: QExactive Plus Orbitrap
That's all at my glimpse,
yours,
Steffen

[JeanFromentNILU]

Hi Thanks, I will work on that later this week. For the Splash, I am retrieving them from PubChem using the WebChem package on R.
Best
Jean

[schymane]

The SPLASH needs to be generated based on your spectral data, not retrieved from PubChem - the SPLASH is a hash of your peaks and should be unique. Perhaps this is why this is leading to problems. Steffen did implement a SPLASH algorithm in R though ... here's an overview in Gert's repo:
https://github.com/berlinguyinca/spectra-hash

[JeanFromentNILU]

Yes sorry, I got confused I am using GetSplashR from R or the splash given by ChemVista

[schymane]

OK good (phew) - that makes more sense!

[meier-rene]

I fixed the remaining issues. Here comes a report of issues I found:

• AC$MASS_SPECTROMETRY: MS_TYPE MS1 -> AC$MASS_SPECTROMETRY: MS_TYPE MS
• AC$MASS_SPECTROMETRY: MS_TYPE and AC$MASS_SPECTROMETRY: ION_MODE were missing in a few records
• AC$COLLISIONENERGY -> AC$MASS_SPECTROMETRY: COLLISION_ENERGY
• The chemical compound annotation of the "Dechlorane" family was not always correct or missing
  I fixed everything. Besides that there is a platform incompatibility of the line ending of the last line between windows and linux. I can easily fix that with a tool but it might be complicated to fix that from windows. Not much You or I can do about it.

[JeanFromentNILU]

Hi, Thanks you very much! I was going to work on it tomorrow but you were much quicker than me! Thanks a lot for the help.

Jean