> 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/file-naming-conventions/lc-ms-metabolomics.md).

# LC-MS Metabolomics

<figure><img src="/files/S4R8qIjQHjyUSfoG4iQV" alt=""><figcaption><p><strong>This file name refers to mass spectrometry file number 23 that was collected in reverse phase on the Lumos in dataset CMP002 (run on 07/21/22).</strong></p></figcaption></figure>

Please use this file naming template for LC-MS Mass Spectrometry tool as a guide to create file names.

{% file src="/files/w6zSh8Hpg2LdDnkHztYw" %}

### Field definitions

Each number in the example above corresponds to a field in the file name. Fields are separated by ‘\_’ to enhance computer readability. Shortened column names used in the template above are provided in parentheses next to the appropriate field definition.

1. Dataset Number (Dataset\_No):
   * All C-CoMP datasets will be assigned an internal dataset number. Please request this number on the #dataset\_number\_requests slack channel following the instructions provided above.
   * Metadata about the dataset (including Dataset number, method type, and data storage location) will be recorded in the [C-CoMP Data Catalog](broken://pages/98cmlcUsIyiEFf8NeN2z).
2. Date (format: mmddyy)
   * The date when the file was generated (the date of the instrument run)
3. Mass Spectrometer (MassSpec\_Type)
   * The type of mass spectrometer used for analysis. Options currently in use: Lumos or Altis
4. Method (Method):
   * Indicate which method was used to run the sample on the instrument. Please choose one of the Method Abbreviations below.
5. File number (File\_No)
   * The file number is the number assigned to each file at the initiation of data collection for the sample relative to the instrument run. The file numbers are generated in numerical order. File numbers (and full file names) are linked to Sample IDs and other metadata (relevant to experiment, field collections, and instrument run conditions) within a ‘Sequence’ spreadsheet. For this datastream, file numbers are used to account for additional standards, controls, and pooled samples that are run along with the biological samples and to build in the ability to re-run samples as needed.
6. File-type extension (File\_type\_ext)

**Mass Spectrometer:**

* Lumos
* TSQ (not active - 7/25/2022)
* Altis

**Method Abbreviations:**

* RP - Reverse Phase
* HL - HILIC
* BC - Benzoyl Chloride
* CO - Carbonyl Method


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