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UniCarb-DR: MIRAGE ベースのグライコミクス MS/MS スペクトルデータリポジトリ
Yushi Takahashi1, Shujiro Okuda2, Masaaki Shiota1, Kiyoko F. Aoki-Kinoshita1
1Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, Tokyo, JAPAN
2Medical AI Center, Niigata University School of Medicine, Niigata, JAPAN

Recently many public data repositories have been rapidly developed to store datasets submitted by researchers and to promote sharing ofsuch data under the FAIR (Findable, Accessible, Interoperability, and Re-usable) data principles. In the glycosciences, the Minimum Information
Required for A Glycomics Experiment (MIRAGE) [1] proposes a set of standard guidelines when reporting qualitative and quantitative results ofglycomics experiments including mass spectrometry, glycan arrays, liquid chromatography, etc. There are two major public data repositories,
UniCarb-DR [2] and GlycoPOST [3], to allow researchers to submit their mass spectrometry-based experimental results following the MIRAGE
guidelines. UniCarb-DR can visualize the MS/MS spectra data submitted by researchers in GlycoWorkbench format (.gwp), and users canbrowse and search each of the spectra and glycan structures in their web browsers. GlycoPOST, on the other hand, can accept various MS
experiment-related resources from researchers including the raw data from mass spectrometers. The researchers can make their data public
after an embargo period; it thus allows them to configure their data publication date freely. However, this functionality is not available in UniCarbDR. In this study, we tried to enhance the integration of these complementary data repositories by unifying the data submission flow and making
it easy to cross-reference.

① Researchers submit their dataincluding GlycoWorkbench files (.gwp)
to GlycoPOST following the MIRAGE
guidelines.

We aimed to integrate the data submission flowusing GlycoPOST’s REST APIs. When researchers
submit their data to GlycoPOST, they can configure
the data publication date freely. Thus, the data cannot
be public until the date (Step ①-②). The UniCarbDR’s batch system will periodically try to fetch all of
the published data from GlycoPOST and store them inthe database of UniCarb-DR (Step ③-⑤). Finally,users can browse the data published in GlycoPOSTon UniCarb-DR and visualize it easily (Step ⑥-⑧).

https://unicarb-dr.glycosmos.org

MIRAGE.gwp
files

https://glycopost.glycosmos.org⑤ Retrieved data will be
registered to UniCarb-DR
in a batch process.

⑥ Thanks to the batch process, now UniCarb-DR canvisualize the data public on GlycoPOST. Users canbrowse the dataset by clicking its title.

② Submitted datacannot be public during
an embargo period.

Published !

③ After the embargo period,
the submitted data will be public
on the GlycoPOST website.

④ Newly published data
will be retrieved withGlycoPOST’s REST APIs.

⑦ All glycan sequences in a
GlycoWorkbench file will bedisplayed. By clicking a glycan
image, users can see moredetailed MS experiment results.

The retention
time and therecorded
precursor
mass data will
also bedisplayed ifpossible.

TheMIRAGE
information

dragousewith mmooZ⑧ Detailed mass spectra peak chart will be displayed.
Users can zoom it with mouse drag. By clicking theGlycoPOST ID (e.g. GPST000009), users can check thecorresponding GlycoPOST entry quickly.

In this study, we propose a new comprehensive glycomics datarepository workflow combining the advantages of two major datarepositories making it easier for users to submit mass spectrometrydata. We are planning to release this new functionality on the next
UniCarb-DR’s release. Both UniCarb-DR and GlycoPOST follow
the MIRAGE guidelines, however, UniCarb-DR collects additional
HPLC settings information, which GlycoPOST does not support at
the time of this writing. Therefore, to integrate the data submission
flow of these two data repositories completely, we are planning to
update GlycoPOST to support the additional HPLC settings
information.

All mass spectra
peaks and thecorresponding
intensity is listed in atable form.

By calculating mass
spectra similarity score,
all similar spectra
stored in UniCarb-DR
will be listed. Users
can browse the spectra
data by clicking each of
the image.

1. York, et al. Glycobiology, 24(5):402–406, 2014.
2. Rojas-Macias, et al. Nature communications, 10(1):3275, 2019.
3. Watanabe, et al. Nucleic Acids Research, 49(D1):D1523-D1528, 2021.
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