Performing the search

Load your .raw files directly into Proteome Discoverer and run a search via the Sequest search wizard.

Importing identification results into Progenesis LC-MS

Note: you will need Excel2007 installed to import the search results

1. In Proteome Discoverer, open a search result file.
2. Right click on a Protein entry in the result table.
3. From the context menu which appears choose to create an Excel .Worksheets.
4. Select options to not leave any blank rows in the exported file.
5. Choose the first 2 options to include Peptide and Protein information.
6. Make sure that “Group the peptides” is not selected.
7. Export the file giving it the same name as the .raw file the results were created from i.e [name].raw becomes [name].xls.
8. Import the Excel file into Progenesis LC-MS in the Peptide Search Stage.

If the Peptide entries in the Excel tables do not contain the "Spectrum File", you will be asked to confirm that the name of the Excel file matches the name of the .raw file from which the search was created.