LabKey Server lets you upload custom lists of proteins. In addition to protein identifiers, you can upload any other data types you wish. For example, you might create a custom list of proteins and quantitation data from published results. Once your list is loaded into the server, you can pull it into MS2 pages as a separate column. This allows you to view, sort, and filter the data.

Uploading Custom Protein Annotations
To add custom protein annotations:

• Navigate to the MS2 Dashboard.
• Select Admin -> Manage Custom Protein Lists.
• Click the Import Custom Protein List button.

(Alternatively, you can follow this path: Admin -> Site -> Admin Console -> Protein Databases -> Load New Annot File.)

You need to upload the annotations in a tab-separated format (TSV). You can include additional values associated with each protein, or just upload a list of proteins.

The first line of the file must be the column headings. The value in the first column must be the name that refers to the protein, based on the type that you select. For example, if you choose IPI as the type, the first column must be the IPI number (without version information). Each protein must be on a separate line.

An easy way to copy a TSV to the clipboard is to use Excel or another spreadsheet program to enter your data, select all the cells, and copy it. You can then paste into the textbox below.

You can download a sample file from the labkey.org server for an example of what a file should look like.

Click on the "Submit" button. Assuming that the upload was successful, you'll be shown the list of all the custom annotation sets.

Note: Upload sets that are loaded directly into a project are visible in all subfolders within that project. If a set within the subfolder has the same name, it masks the set in the project.

Viewing Your Annotations
Click on the name of the set to view its contents. You'll see a grid with all of the data that you uploaded.

To see which the proteins in your custom set match up with a protein that the server has already loaded from a FASTA or Uniprot file, click on the "Show with matching proteins loaded into this server" link.

Using Your Annotations
You can add your custom annotations to many of the MS2 pages. To see them while viewing a MS2 run, select the Query - Peptides grouping. Click on the "Customize View" link. If you want to use the search engine-assigned protein, expand the Search Engine Protein->Custom Annotations node in the tree. For a ProteinProphet assigned protein, expand the Protein Prophet Data->Protein Group->First Protein->Custom Annotations node. Expand the node for your custom annotation set. Lookup String is the name you used for the protein in your uploaded file. Select the properties you want to add to the grid, and click Save. They will then show up in the grid.

You can also add your custom annotations to other views using the Customize View page. When viewing a single MS2 run under the Query - Protein Groups grouping, expand the Proteins->Protein->Custom Annotations node. When viewing Protein Search results, in the list of protein groups expand the First Protein->Custom Annotations node. In the Compare Runs query view, expand the Protein->Custom Annotations node.