Empa Air Pollution #347
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 ;) |
| AC$CHROMATOGRAPHY: KOVATS_RTI 818 | ||
| PK$SPLASH: splash10-000t-9000000000-90ef1466a5c67cf33c97 | ||
| PK$ANNOTATION: m/z formula_count exact_mass error(ppm) tentative_formula intensity_fraction | ||
| 49.98421 1 49.99178 151.43 H3CCl+ 0.76 |
There was a problem hiding this comment.
delete or review. unlikely to be H3CCl+ from structure and if so missing isotope signal
| 69.94142 1 69.93716 -60.95 Cl2+ 1.00 | ||
| 71.93848 1 71.93421 -59.40 Cl[37Cl]+ 0.77 | ||
| 81.94018 1 81.93716 -36.89 CCl2+ 1.00 | ||
| 83.94540 1 83.93421 -133.34 CCl[37Cl]+ 0.60 |
There was a problem hiding this comment.
this is weird, twice in a row 83.94540 m/z with two different assignments? Also, NIST spectrum has strong signal at 83 m/z HCCl2, but here it is absent?
There was a problem hiding this comment.
Why are generally more than one formula assigned to a given mass? I see that up to 3 formulas assigned per formula for this compound (some other compounds have up to 4 assignments. Do we want that? Seems weird to me
| 81.94018 1 81.93716 -36.89 CCl2+ 1.00 | ||
| 83.94540 1 83.93421 -133.34 CCl[37Cl]+ 0.60 | ||
| 83.94540 2 83.95281 88.23 H2CCl2+ 0.86 | ||
| 85.94626 1 85.94986 41.85 H2CCl[37Cl]+ 1.00 |
There was a problem hiding this comment.
NIST has a strong 85 m/z signal (maybe H3CCl2)...but it is absent here? --> OH no I see that the unassigned peaks are listed separately below...but this seems silly to me that two of the most abundant peaks 83 and 85 m/z are not assigned and not listed here...
| 93.93877 1 93.93716 -17.17 C2Cl2+ 0.57 | ||
| 94.94653 1 94.94498 -16.31 HC2Cl2+ 1.00 | ||
| 95.95457 1 95.94834 -64.96 HC[13C]Cl2+ 0.01 | ||
| 95.95457 2 95.95281 -18.37 H2C2Cl2+ 1.00 |
There was a problem hiding this comment.
how is number 1 and number 2 assignment decided? It looks like intensity_fraction shows how much of the mass is assignable to the formula, wouldn't it make more sense to have the higher intensity_fraction assigned as 1?
| AC$CHROMATOGRAPHY: KOVATS_RTI 566 | ||
| PK$SPLASH: splash10-002o-9000000000-17c33adb4eb05f58d77f | ||
| PK$ANNOTATION: m/z formula_count exact_mass error(ppm) tentative_formula intensity_fraction | ||
| 23.98798 1 0.00000 0.00 - 0.00 |
There was a problem hiding this comment.
what's happening here? something seems wrong...
| 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.
ok but weird how the ppm error is so much worse for the higher masses --> maybe need to redo postprocessing calibration for this spectrum?
There was a problem hiding this comment.
ok, BUT 64.01073 H2C2F2+, 51.00434 HCF2+ missing the 13C isotope peak
There was a problem hiding this comment.
HFO-1234zeE
compare to HFO-1234yf:
There was a problem hiding this comment.
ok but why does 83.00812 H2C2F3+ not have 13C-isotope peak?
There was a problem hiding this comment.
ok. E- and Z- isomers should probably be identifical. If there are differences that might scew i.d. of one or the other in pipeline, but really shouldn't be able to tell from spectrum
There was a problem hiding this comment.
ok BUT what are those missing peaks at ca. 30 m/z?
There was a problem hiding this comment.
ok BUT why missing 13C-isotope signals??? re-extract?
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.
Probably missing ions because of notching?
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.
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.
91.92426 CHBr and 63.00276 CH2F2 are a little more off 20 ppm should also be annotated as large peaks
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
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 ;)