Creating a ProteinPilot Software Winner Proteins Results List as FASTA File

1. In ProteinPilot™ software, review the section of the Protein Summary Report that corresponds to the FDR Type Global and the FDR of 1%. In the example below, 2798 proteins are showing as the total in the ID Yield column.

2. Create a Protein Summary .txt file from the Protein Summary Results file.

3. Open the Protein Summary in Excel and keep only the 1% global FDR proteins. This protein list needs to be copied into a new sheet. 

4. The protein accession numbers in the list can be used to create a FASTA file at UniProt using this link: https://www.uniprot.org/uploadlists/.

5. Follow the steps in the images below to create the uncompressed FASTA file.






6. Save the list as uncompressed FASTA file.