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meier-rene merged 14 commits into from
Jan 13, 2026
Merged

Initial commit of 14 spectra from Qingdao_University #365

meier-rene merged 14 commits into from
Jan 13, 2026

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@meier-rene meier-rene commented Jan 7, 2026

This is a PR for 14 spectra from Qingdao University.

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meier-rene commented Jan 7, 2026

Hi Cuili,
in this PR we can discuss all questions and open issues. At first we have to decide how to add Qingdao University to our list of contributor https://github.com/MassBank/MassBank-data/blob/dev/List_of_Contributors_Prefixes_and_Projects.md. We could simply add a line:
Qingdao_University | Qingdao University, Qingdao | China | QDU |
But you can modify that if you want.

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meier-rene commented Jan 7, 2026

And here are some additional information provided by Cuili.
all_spectra.pdf
compoundlist.csv

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meier-rene commented Jan 7, 2026

From the check I can see that the RECORD_TITLE line does not follow our spec. You can find the record format specification in https://github.com/MassBank/MassBank-documentation/blob/dev/MassBankRecordFormat.md. The RECORD TITLE also contains the instrument type. You gave LC-ESI-Orbitrap as instrument type, but thats not an allowed value for the instrument type. It can be either LC-ESI-QFT or LC-ESI-ITFT. But you did not specify the model, so I need more information to help you here. A proper example for a title could be:
RECORD_TITLE: diethylprop-1-en-2-ylphosphate; LC-ESI-QFT; MS2; 15 eV; [M-H]-

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zcl20009 commented Jan 8, 2026

Dear Mr. Meier，
thank you for your review and feedback. I have checked the relevant specifications. The instrument I used is the Thermo Scientific Orbitrap 480, configured as a quadrupole-Orbitrap tandem mass spectrometer (Q-Orbitrap). Could you please confirm if, based on this configuration, it should be classified as LC-ESI-QFT? If so, I will proceed to correct the RECORD_TITLE accordingly.

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meier-rene commented Jan 8, 2026

Thank you for the information. Yes, the instrument type in MassBank would be a LC-ESI-QFT.

I don't know if you are familiar with the concepts of git, that's why I will give you a little explanation: If you want to add or change anything on the files in this pull request, you would need to work on my fork of the data at https://github.com/meier-rene/MassBank-data. I invited you to the repo, which should give you access. Every change you do in the fork will end up automatically in this PR. For now I will go ahead and introduce the information you gave into your data files.

In addition to that, I also need your approval or suggestions for the contributor list.

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meier-rene commented Jan 8, 2026

I made a few changes/fixes to the metadata of your spectra. The changes are :

  • modified instrument type, record title and instrument as discussed
  • changed ion mode to NEGATIVE
  • add two spaces in front of peak list values
  • added correct splash
  • changed formula to our spec

They now conform to the record format.

Maybe we could improve the metadata a little bit. I have a few questions:

  • What is the source of the compounds you measured. Are they original standards?
  • Can you can specify the solvent/gradient of your UPLC? This would make the retention time more valuable.

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zcl20009 commented Jan 8, 2026

Thank you for the updates. As requested, please find the detailed metadata information below:

  1. Compound source clarification: The compounds detected were identified in an extract from the electrode materials of spent lithium-ion battery cells (NMC type), and were not analyzed using commercial reference standards.
    2.Chromatographic method details:
    Mobile Phase: (A) Methanol; (B) Deionized water with 0.1% formic acid.
    Gradient Elution Profile:
    0 min: 95% B;
    1.0 min: 95% B;
    1.5 min: 20% B;
    4.0 min: 20% B;
    4.1 min: 0% B;
    8.0 min: 0% B;
    10.0 min: 95% B.

Please also find our contributor list as follows:
Cuili Zhang, Hongna Zhang, Pengfei Wu, Bing Wang, Yating Xiao, Xinxin Gu, Yongbiao Wan, Ming Li, Yongfeng Lin, Wei Gao, Xiaoran Wei, Juntong Wei, Yuxin Zheng.

Should you require a detailed breakdown of author contributions or any further particulars, we are happy to provide them at any time.

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meier-rene commented Jan 12, 2026

I added the chromatographic information you provided. Can you also specify the flow rate of the gradient?

Did I understand you correctly that the contributor list you provided should be added to the author list of the spectra?

Because you did not use a reference compound for identification I ask you to check https://pubs.acs.org/doi/10.1021/es5002105 and tell me what level of structure identification you have.

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zcl20009 commented Jan 12, 2026

Thank you for your follow-up. Regarding your questions:

  1. The chromatographic flow rate was 0.3 mL/min.

  2. You are correct—the contributor list I provided should be added as the author information for these mass spectra.

  3. For the confidence level of compound identification, we strictly followed the criteria outlined in the reference you shared (10.1021/es5002105). Detailed identification levels have been included in the attached “compoundlist” table for your review.

compoundlist.csv

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zcl20009 commented Jan 12, 2026 via email

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zcl20009 commented Jan 13, 2026

Dear Rene,

Thank you again for your guidance and assistance throughout the metadata revision process.

Could you please let me know if any further information or adjustments are needed from my side?

Additionally, if the submission is now complete, could you confirm whether the data has been successfully uploaded to the MassBank database? If so, kindly advise on how I can locate or access the records—for example, whether they can be retrieved via the compound name, accession number, or other identifiers.

I appreciate your support and look forward to your update.

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meier-rene commented Jan 13, 2026

Dear Ciuli,
I think the contribution is complete now. From your message I understand that you want to get this public asap. I will merge this PR to our data repository now. I can also upload the new data to our development and test server after that. I will provide a link to this server. You could then access your data there for review and it would be findable by accession, by compound or name.

On the official server at massbank.eu or massbank.jp your data will arrive after the next data release. These releases happen at least two times a year but if people request it, we can do it more frequently. There is no fixed schedule. I have another pull request open which sounds urgent. So I will at least merge this one as well and then I can prepare a release and we could upload this to the official servers. If you prepare a manuscript atm and want to show this right now, you are restricted to the development server. But you can already refer to the accession because we wont change them after your data has been merged.
Best, Rene

@meier-rene meier-rene merged commit 88e8607 into MassBank:dev Jan 13, 2026
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meier-rene pushed a commit that referenced this pull request Jan 13, 2026
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14 spectra from Qingdao_University (#365)
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zcl20009 commented Jan 13, 2026 via email

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meier-rene commented Jan 14, 2026

Hi Cuili,
I uploaded your data to the testserver and you can review your files with this link: https://msbi.ipb-halle.de/MassBank3/search?contributor=Qingdao_University
The correct way to cite the data is:
DOI 10.5281/zenodo.3378723
and for the whole MassBank use:
Steffen Neumann, René Meier, Michael Wenk, Anjana Elapavalore, Takaaki Nishioka, Tobias Schulze, Michael Stravs, Hiroshi Tsugawa, Fumio Matsuda, Emma L Schymanski, MassBank: an open and FAIR mass spectral data resource, Nucleic Acids Research, 2025;, gkaf1193, https://doi.org/10.1093/nar/gkaf1193

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zcl20009 commented Jan 15, 2026

Dear Rene,

Thank you for your efficient work and for sharing the test server link. We have begun reviewing the uploaded data.

We would like to kindly confirm two follow-up points with you:

Are the accession numbers for our dataset now finally assigned?

Will our data be included in the next updated version of the Zenodo DOI (10.5281/zenodo.3378723)?

We look forward to your reply. Thank you again for all your support!

Best regards,
Cuili

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zcl20009 commented Jan 15, 2026 via email

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meier-rene commented Jan 15, 2026

Yes, accessions are final if you don't want any changes on the accessions and the data will be in the next release.

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zcl20009 commented Jan 15, 2026 via email

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