Empa Air Pollution #347

lionel42 · 2025-11-06T10:01:01Z

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 · 2025-11-06T12:50:00Z

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 · 2025-11-06T12:50:57Z

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

schymane · 2025-11-06T16:24:55Z

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 · 2025-11-06T16:34:22Z

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 · 2025-11-17T15:28:58Z

@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 · 2025-12-10T07:38:42Z

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 · 2025-12-10T14:48:15Z

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 · 2026-01-01T17:06:00Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__1_1_2_TRICHLOROETHANE.txt

+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


delete or review. unlikely to be H3CCl+ from structure and if so missing isotope signal

Alina-beal · 2026-01-01T17:16:57Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__1_1_2_TRICHLOROETHANE.txt

+  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


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?

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

Alina-beal · 2026-01-01T17:23:31Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__1_1_2_TRICHLOROETHANE.txt

+  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


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...

Alina-beal · 2026-01-01T17:28:51Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__1_1_DICHLOROETHENE.txt

+  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


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?

Alina-beal · 2026-01-01T17:35:36Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__1_CHLORO_1_PROPENEE.txt

+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


what's happening here? something seems wrong...

Alina-beal · 2026-01-01T17:36:00Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__2_CHLORO_1_PROPENE.txt

+AC$CHROMATOGRAPHY: KOVATS_RTI 536
+PK$SPLASH: splash10-002o-9000000000-47ee5923217847ad72ce
+PK$ANNOTATION: m/z formula_count exact_mass error(ppm) tentative_formula intensity_fraction
+  23.98803 1 0.00000 0.00 - 0.00


here there is also something wrong all 0s

Alina-beal · 2026-01-01T17:37:45Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__CHLOROETHENE.txt

+AC$CHROMATOGRAPHY: KOVATS_RTI 415
+PK$SPLASH: splash10-03fr-9000000000-a2695f0ec68bc37ebdd1
+PK$ANNOTATION: m/z formula_count exact_mass error(ppm) tentative_formula intensity_fraction
+  23.98785 1 0.00000 0.00 - 0.00


all 0s problem

Alina-beal · 2026-01-01T17:38:18Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__C_C4F8O.txt

+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


so many peaks and so few assignments, what's going on here?

Alina-beal · 2026-01-01T18:08:50Z

Empa_Air_Pollution/MSBNK-Empa_Air_Pollution-EAP__ETHANE.txt

+AC$CHROMATOGRAPHY: KOVATS_RTI 200
+PK$SPLASH: splash10-004i-9000000000-bf642cfd2c96c56eb2e0
+PK$ANNOTATION: m/z formula_count exact_mass error(ppm) tentative_formula intensity_fraction
+  26.01452 1 0.00000 0.00 - 1.00


something wrong many 0s

lionel42 added 4 commits November 6, 2025 10:55

upload test spectras

1288f31

fix accession top

79042d0

fix date format

4638246

adding us in contributers

061e68e

lionel42 mentioned this pull request Nov 6, 2025

Help for adding new compounds #348

Open

lionel42 added 2 commits November 17, 2025 15:20

fix formatting issues

85f1b70

fix format

8823376

lionel42 added 3 commits November 19, 2025 18:15

adding identification outputs

a23eaa4

update all specs

831e78a

fix various spectra

9531e9e

lionel42 added 5 commits December 10, 2025 16:12

fix COS with larger uncertainty for annotations

89f3c3f

fixed name from database

d0a8ac0

adding missing specs

4bcae78

adding also unidentifed masses in annotations

4fb5fe9

adding kr

6ec740c

Alina-beal reviewed Jan 1, 2026

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Empa Air Pollution #347

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Empa Air Pollution #347

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lionel42 commented Nov 6, 2025

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lionel42 commented Nov 6, 2025

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lionel42 commented Nov 6, 2025

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schymane commented Nov 6, 2025

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schymane commented Nov 6, 2025

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lionel42 commented Nov 17, 2025

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meier-rene commented Dec 10, 2025

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lionel42 commented Dec 10, 2025

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