Why doesn't a TrEMBL FASTA file work for a ProteinPilot search?

For research use only. Not for use in diagnostic procedures.

Answer

The TrEMBL database http://www.ebi.ac.uk/uniprot/TrEMBLdocs/trembl_release_notes_13.html) is computer-annotated protein sequence database  and not reviewed and could contain redundancies in terms of protein sequences, protein ascension numbers, etc. This database is not recommended for use with ProteinPilot™ software. 

Below are some of the main factors to consider before choosing a database to search within ProteinPilot software:

• Provider of the database: EBI, NCBI, species consortia, TrEMBLE, etc.
• Species constraints: exact species, similar species or everything?
• Elaboration of sequences: include isoforms, or exclude unnecessarily redundant sequences?
• Maximize sensitivity and specificity of the search by: A) including high numbers of proteins that could be in the sample; or B) excluding high numbers of proteins unlikely to be in the sample.