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