Empa Air Pollution#347
Conversation
|
I have opened an issue for asking help. I will be away for one week (holidays) so I will continue working on this later on. |
|
One point that i find wierd is that the validator seems to not like the Accession strings |
You can find the details about how to construct the Accession IDs here: It appears that you've put the name in the Accession, whereas we expect a number, e.g.: |
Please note that we have detailed record specifications to help explain what is needed in the various record entries: It seems from the validation output that at least one other compulsory field is missing: The IPB Halle team are at BioHackEU25 this week, so they are a bit distracted, but will look into this once they are back. |
|
@schymane Thanks for the answers, I managed to fix the format of our files. Before I add the whole library, is it possible to confirm/register our laboratory and the prefix ? do you need any additional information from our side ? |
|
Hi Lionel, |
Hi Rene, Thanks for reaching out, we would still need more time (we want to go manually though all files to do a quality check. About the table of contributors, we discussed and suggest the following :
I had initially also changed in the file in the PR, should I do it this way or do you want to update it from a separate PR ? We will notify you when ready to merge ;) |
| 93.93877 1 93.93716 -17.17 C2Cl2+ 0.57 | ||
| 94.94653 1 94.94498 -16.31 HC2Cl2+ 1.00 | ||
| 95.95457 1 95.94834 -64.96 HC[13C]Cl2+ 0.01 | ||
| 95.95457 2 95.95281 -18.37 H2C2Cl2+ 1.00 |
There was a problem hiding this comment.
how is number 1 and number 2 assignment decided? It looks like intensity_fraction shows how much of the mass is assignable to the formula, wouldn't it make more sense to have the higher intensity_fraction assigned as 1?
| AC$CHROMATOGRAPHY: KOVATS_RTI 396 | ||
| PK$SPLASH: splash10-0udi-3900000000-5d7701f39c27b4d50277 | ||
| PK$ANNOTATION: m/z formula_count exact_mass error(ppm) tentative_formula intensity_fraction | ||
| 42.99847 1 42.99785 -14.31 C2F+ 0.98 |
There was a problem hiding this comment.
so many peaks and so few assignments, what's going on here?
There was a problem hiding this comment.
can we amend that it is PFC-318 for the mygu spectrum to be consistent with NIST? that's also how we have it stored on the instruments
|
There are quite a few spectra missing from the MC-2021A and B batches: Can you double check that
|
There was a problem hiding this comment.
some missing 13C isotope signals and what are those very high masses at low intensity?
232.9605
251.95248
253.94708
269.90825
There was a problem hiding this comment.
only see double ions? maybe retract this spectrum
There was a problem hiding this comment.
missing 33 m/z ion from F+, filtered out?
There was a problem hiding this comment.
ok but missing some 13C isotope signals
There was a problem hiding this comment.
missing the double 37Cl isotope peak from 93.93638 C2Cl2+ at +4 and all the Cl-containing signals below m/z 70 are missing their 37Cl isotope peaks
There was a problem hiding this comment.
missing 34S isotope signals for lower masses
| PROJECT: HALOHUNTER Discovering halogenated compounds in the atmosphere with non-target screening of preconcentrated air samples | ||
| CH$NAME: 1,2-dichloroethene, E | ||
| CH$NAME: 1,2-dichloroetheneE | ||
| CH$NAME: HFO-1330E |
There was a problem hiding this comment.
Is this name correct @Alina-beal ? Should have a fluor to be HFO right ?
4 participants
Hello,
We are the laboratory for Air Pollution of Empa and we would like to contribute to MassBank with our spectras.
I wanted to test the format locally but ran into issues with the check software. see MassBank/MassBank-web#414 and MassBank/MassBank-web#413
This is just a draft for now, we have hundreds of spectra to upload, but we wanted first to ask about the format and the metatdata.
I created names and identifiers for our lab: EAP for Empa Air Pollution
Happy to receive any feedback ;)