How do I run an MS/MS ion search?

You can run ion searches by exporting peak list files to a protein identification program. Search results files may then be imported back in to link protein IDs to detected peaks.

Exporting the query file

1. Choose which ms/ms spectra to export
2. Choose your protein ID program in the drop down list to ensure that files are exported and imported in the correct format
3. Click the 'Export current query set' button to export the chosen queries in one of the supported formats.
4. Use the exported file(s) to run searches in your protein ID program

Importing search results

1. Export search results in the format used by your selected search program. (See the supported formats page for details of the format used by each program.)
2. Click on the 'Import search results' button to import results files.