Empa Air Pollution

[lionel42]

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 ;)

[lionel42]

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.

[lionel42]

One point that i find wierd is that the validator seems to not like the Accession strings

[schymane]

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:
https://github.com/MassBank/MassBank-web/blob/main/Documentation/MassBankRecordFormat.md#2.1.1

It appears that you've put the name in the Accession, whereas we expect a number, e.g.: ACCESSION: MSBNK-AAFC-AC000101

[schymane]

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.

Please note that we have detailed record specifications to help explain what is needed in the various record entries:
https://github.com/MassBank/MassBank-web/blob/main/Documentation/MassBankRecordFormat.md#table-1--massbank-record-format-summary
...and then lots of details and examples in subsequent subsections.

It seems from the validation output that at least one other compulsory field is missing: AC$INSTRUMENT

The IPB Halle team are at BioHackEU25 this week, so they are a bit distracted, but will look into this once they are back.

[lionel42]

@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 ?

[meier-rene]

Hi Lionel,
do you consider this contribution as complete? At the moment there are just two little issues left. One space too much and an empty table with peak annotations which needs to go. If yes, I can finish this minor things and merge your contribution. We also maintain a table with our contributors: https://github.com/MassBank/MassBank-data/blob/dev/List_of_Contributors_Prefixes_and_Projects.md. It would be welcome if you tell me what you want to see there or I will guess something for you.
Best, Rene

[lionel42]

Hi Lionel, do you consider this contribution as complete? At the moment there are just two little issues left. One space too much and an empty table with peak annotations which needs to go. If yes, I can finish this minor things and merge your contribution. We also maintain a table with our contributors: https://github.com/MassBank/MassBank-data/blob/dev/List_of_Contributors_Prefixes_and_Projects.md. It would be welcome if you tell me what you want to see there or I will guess something for you. Best, Rene

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.
Also we build them automatically, so I will try to fix the 2 issues in our code.

About the table of contributors, we discussed and suggest the following :

• Database: Empa_Air_Pollution
• Research Group / Research Project: Empa - Laboratory for Air Pollution / Environmental Technology
• Country: Switzerland
• Prefix of ID: EAP
• Project Tag: HALOHUNTER

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 ;)

[Alina-beal]

i just wanted to comment but accidentally started a review i dont know whats the difference

[Alina-beal]

HCFC-132a, in MC-2019D: 1,1-dichloro-2,2-difluoroethane https://webbook.nist.gov/cgi/cbook.cgi?ID=C471432&Units=SI
HCFC-132b, in MC-2019D: 1,2-dichloro-1,1-difluoroethane https://webbook.nist.gov/cgi/cbook.cgi?ID=C1649087&Units=SI
HCFC-132c, in MC-2019C: 1,1-dichloro-1,2-difluoroethane, no NIST spectrum
HCFC-132, in MC-2019C: 1,2-dichloro-1,2-difluoroethane, no NIST spectrum

HCFC-123a, no mygu: is 1,2-Dichloro-1,1,2-trifluoroethane, https://webbook.nist.gov/cgi/cbook.cgi?ID=C354234&Units=SI
HCFC-123b, no mygu: is 1,1-Dichloro-1,2,2-trifluoroethane
HCFC-123, in a flask COC...: is 2,2-Dichloro-1,1,1-trifluoroethane, https://webbook.nist.gov/cgi/cbook.cgi?ID=C306832&Units=SI

looks like all the NIST are there, but we don't have the HCFC-123 mygu extracted. However it's in COC 525213 I don't know if I measured it

[Alina-beal]

wow ours looks really different in intensities than NIST, it's not necessarily wrong

intact ions are not i.d. correctly why? it's only 4 ppm mass error very good
133.95080 1 0.00000 0.00 - 1.00
134.95232 1 0.00000 0.00 - 1.00
135.94778 1 0.00000 0.00 - 1.00
136.01781 1 0.00000 0.00 - 1.00
136.95141 1 0.00000 0.00 - 1.00
137.94486 1 0.00000 0.00 - 1.00

in the spectrum around mass 85 m/z the Cl:Cl[37] isotope ratio should be 3:1, in spectrum it doesnt look like that at all but in the peak list it does, not sure what's going on
84.96559 1 84.96511 -5.64 CF2Cl+ 1.00
86.96259 1 86.96216 -4.94 CF2[37Cl]+ 0.99

[lionel42]

This is very suspicious, should we investigate if there is no coelution in that sample ?

[Alina-beal]

oops

[Alina-beal]

hmmm some isotope signals appear to be missing and masses in the range of 90 m/z not the best spectrum

[lionel42]

Should we extract somewhere else ?

[sneumann]

Hi, thanks for your contribution !
Just a side note, in addition to the validator here in GitHub, we also have an online Validator for individual records that you can copy&paste at: https://massbank.eu/MassBank/service
We probably need to advertise that more in the documentation.
Yours, Steffen