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How to cite GlycoPOST

Yu Watanabe, Kiyoko F Aoki-Kinoshita, Yasushi Ishihama, Shujiro Okuda, GlycoPOST realizes FAIR principles for glycomics mass spectrometry data, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D1523–D1528, https://doi.org/10.1093/nar/gkaa1012

Before submission

Preparing for submission

You have to sign in with a verified email address to submit data.
Please visit GlycoPOST / UniCarb-DR User account service and sign up for the repositories. The service will send you an email containing a specific token. By entering the token, you can verify your email address. If you have lost that email, you can resend it from the service.

Our submission tool outline

submission_fig

Our submission procedure has two major steps - "Project and file(PROJECT)" and "Preset experimental procedure(PRESET)."

In the PRESET step, input the information about experimental procedure and then assign them to files in the PROJECT section.

If you have a group of files for one paper, you should create a project and upload files for it. Files always belong to one project.

Preset profiles don't belong to a particular project but to a user, so that you can reuse them if you use the same experimental procedure in another project.

flow_fig

Preset experimental procedure

You can click "Submit" button on the menu and then click "Preset experimental procedure" button to configure your presets.

submission_top

PRESET section has five categories - "Sample preparation", "General features", "Ion sources", "Ion transfer optics", "Spectrum and peak list generation and annotation".
Each category is independent and can freely be combined and assigned to a file from the PROJECT section later.

preset_menu

Sample preparation preset

To create a new PRESET profile for sample, click the "Add new preset" button and fill out the forms.

If you can't find the appropriate item in the list, click "Looking for more items" and you can search the whole ontology list.

preset_input

You don't need to fill out all of the items, but some are required. A warning message will be shown if a required item is left empty when you click "Confirm" button.

preset_confirm

Note that you cannot edit or remove the PRESET profile after the assigned file is displayed.

General features preset

To create a new preset for General features, select "General features" tab and click the "Add new preset" button and fill out the forms.

Ion sources preset

To create a new preset for Ion sources, select "Ion sources" tab and click the "Add new presest" button and fill out the forms.

Ion transfer optics

To create a new preset for Ion transfer optics, select "Ion transfer optics" tab and click the "Add new preset" button and fill out the forms.

Spectrum and peak list generation and annotation

To create a new preset for Spectrum and peak list generation and annotation, select "Spectrum and peak list generation and annotation" tab and click the "Add new preset" button and fill out the forms. This preset category is available only for MS/MS experiment.

This preset category is optional.

Liquid chromatography

To create a new preset for Liquid chromatography, select "Liquid chromatography" tab and click the "Add new preset" button and fill out the forms.

This preset category is optional.

Project and file

When you deposit your data, you can create your project for the data. Every project must have an announcement date and at that time it will be publicly available.

You can create a new project by clicking "Add new project" button or edit your ongoing project from "Select" button on the project table.

project_submit_top

First, input the information about your project. Then go to "Select files" step.

project_step_nav

In the "Select files" section, you can apply your registered presets to files you want to upload. The uploaded files are applied to the presets in four categories such as "Raw data", "Peak list", "Identification results", and "Others".

file_type_tab

Raw data

(*Required)

When you apply "Raw data" files, go to the following steps.
Select PRESET profile from each PRESET categories (Sample preparation, General features, Ion sources, Ion transfer optics, Spectrum and peak list generation and annotation). Selected profiles are applied to files by dropping below.

file_profile

Select files for the project from your computer.
You can drag and drop files into the box or click the box and select from dialog (Our system is not able to process the directory).

drag_drop

You can edit file profiles from the list at the bottom. Select target file(s) and apply, add profile information or remove the file. If you want to remove all the files from the project, click the "Reset" button.

apply_profile

Peak list

(*Optional)

You can drag and drop your files into the box or click the box to select files.

Identification results

(*Required)

You can drag and drop your files into the box or click the box to select files.
Any format (e.g. GlycoWorkbench(.gwp), MS Excel, Plain text, etc.) is acceptable.

Others

(*Optional)

You can drag and drop your files into the box or click the box to select files.

File upload

Go to the "Upload files" menu, you can upload your files to the GlycoPOST server.
It may take a while in the case of uploading a large quantities of files.

file_upload

Note that you are not able to edit or remove the any part of the project after the announcement date.

Confirmation

To complete the submission process, go to "Confirmation" menu. If your uploaded files and applied presets passed our check, you can submit your project to the GlycoPOST server and then you can obtain the project ID. If the uploaded files and applied presets don't pass the check, you need to modify them to go back to the previous processes.

project_confirm

Publish project

GlycoPOST has the "embargo" function and the announcement date is set to 1 year later by default.

To publish the confirmed project, enter the new announcement date at Mypage. There is a "Change announcement date" button in the projects table and a textbox will appear by pressing the button. If you want to announce the project immediately, just enter today's date there and click the "Update" button.

MIRAGE Excel file

Experimental procedure presets are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.
MIRAGE Excel file template is here.

Import

To import data from a MIRAGE Excel file, click the "Import MIRAGE Excel File" button on the preset page to go to the import page. Select the Excel file from your computer and click the "Read File" button. If there are no problems with the previewed data, click the "Import" button. The imported data will be registered as one or more presets in GlycoPOST.

Export

To export the MIRAGE format Excel file, click the "MIRAGE" button at the right end of the Project list table on Mypage. The experimental conditions of the files included in the project are exported as a MIRAGE Excel file.

My page

An overview of your submission is available at My page.

Project list

All revisions of all projects are listed in the project table.
You can jump to the submission page by clicking the "edit" button if the project is in editing.
Project ID in the project list table links to the file list page.

mypage_project_edit

Set Announcement date and PubMed ID / DOI

You can update the announcement date and PubMed ID / DOI of submitted project from this list.
If the revision is the latest and is submitted, "Add Publication ID" button and "Change announcement date" button appear. Textbox will be appeared by pressing the button.

input_announcement_date

If the Publication ID is not set after the announcement, you can input it only once in the same way.

Revise

If you want to revise submitted project, press the "Revise" button in the project table (this button appears for the latest and submitted revision).
You can set the new announcement date for the next revision during the revise process.
It may take a while to revise the project with large amount of data.
The GlycoPOST ID will be taken over from the previous revision.

revised_project

FAQ

I want to show my project and files to the reviewer before announcement date.

Click the "Request preview code" button in the project list table in My page.
You can get a temporary URL for your project and a four digit code to access that page for reviewers.
You cannot request preview code for the revision in editing.

My personal information has changed.

You can edit your email address, name, affiliation, ORCID and password from the GlycoPOST / UniCarb-DR User account service.

Cannot edit or remove project, preset, etc.

To edit or remove data already announced is not allowed with the exception of the PubMed ID or DOI. If you have any problem with that, please contact us.

Do we obtain the human sample information such as age and gender for deposited data?

Since human samples deposited to GlycoPOST have unlinked anonymized metadata including age and gender, you can get these information from "Note" in "Sample preparation" preset or "other files".