LabKey Server allows you to quickly search for specific proteins within the protein datasets that have been uploaded to a folder.

Performing a Protein Search

There are a number of different places where you can initiate a search. If your folder is configured as an MS2 folder, there will be a Protein Search web part on the MS2 Dashboard. You can also add the Protein Search web part to the portal page on other folder types, or click on the MS2 tab within your folder.

Type in the name of the protein. The server will search for all of the proteins that have a matching annotation within the server. Sources of protein information include FASTA files and UniProt XML files. See Loading Public Protein Annotation Files for more details.

You may also specify a minimum ProteinProphet probability or a maximum ProteinProphet error rate filter to filter out low-confidence matches. You can also indicate whether subfolders of the current folder or project should be included in the search and whether or not to only include exact name matches. If you do not restrict to exact matches, the server will include proteins that start with the name you entered.

To add a custom filter on your search results, select the radio button and click Create or edit view to select columns, filters, and sorts to apply to your search results.

Understanding the Search Results

The results page is divided into two sections.

The top section shows all of the proteins that match the name, regardless of whether they have been found in a run. This is useful for making sure that you typed the name of the protein correctly.

The bottom section shows all of the ProteinProphet protein groups that match the search criteria. A group is included if it contains one or more proteins that match. From the results, you can jump directly to the protein group details, to the run, or to the folder.

You can customize either section to include more details, or export them for analysis on other tools.

Mass Spec Search Web Part

If you will be searching for both proteins and peptides in a given folder, you may find it convenient to add the Mass Spec Search (Tabbed) web part which combines Protein Search and Peptide Search in a single tabbed web part.

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