> 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-proteomics.md).

# LC-MS Proteomics

<figure><img src="/files/tEtAuGQfBMwy1h1oekSz" alt=""><figcaption><p>This file name refers to culture sample 32 (SA32) that was collected using untargeted proteomics on the QE mass spectrometer in dataset CCMP002. The SA prefix was used before the numerical sample ID in this context to help distinguish sample ID from the file number field that is used for other data streams.</p></figcaption></figure>

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

{% file src="/files/dRzd2EgSiu2GERHurZMn" %}

### 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.
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:  either QE or FN (Fusion)
   * QE is typically used for culture analyses and the Fusion is typically used for metaproteomics
4. Method (Method):
   * Lab-specific instrument run conditions (either 1DDDA, 2DDDA, or 1DDIA)
5. Sample ID (SA\_ID)
   * Sample ID is the discrete identifier that is assigned to each sample. For this data stream, Sample ID is used in the file name to identify samples instead of file number according to existing lab protocols for this data stream. This field uses the convention SA## if the Sample ID is numerical to help distinguish this field from the file numbers that are used in other data streams. If the Sample ID is descriptive (not only numerical), the SA prefix does not need to be used.&#x20;
6. File-type extension

**Instrument run parameters/methods**

* 1DDDA -&#x20;
* 2DDDA - Field samples (untargeted proteomics)
* 1DDIA - Culture samples (untargeted proteomics)


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