> For the complete documentation index, see [llms.txt](https://c-comp.gitbook.io/data-management-handbook/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://c-comp.gitbook.io/data-management-handbook/data-deposition-instructions/raw-and-derived-data-files/lc-ms-metabolomics.md).

# LC-MS Metabolomics

C-CoMP will use the EMBL-EBI [MetaboLights](https://www.ebi.ac.uk/metabolights/) repository to host raw and derived targeted and untargeted LC-MS Metabolomics data generated by C-CoMP.

General directions

1. Create a MetaboLights account (if you do not already have one) and log in.
2. Click on the ‘Submit Study’ button to begin the submission process.
   * You can use this button to submit a new study or update an existing study.
3. If you create a new study, you will need to complete the following tasks:
   1. Upload raw and derived files.
      * You will need to use FTP or Aspera to upload your raw and derived files. 
   2. Complete the study description.
   3. Complete the sample and assay information description.

After submission, the MetaboLights team will curate your study and ask for additional information. MetaboLights can generate ‘reviewer links’ for studies that are not public.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://c-comp.gitbook.io/data-management-handbook/data-deposition-instructions/raw-and-derived-data-files/lc-ms-metabolomics.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.