While XML files are strongly encouraged for database creation, you can also use FASTA files in ProSightPD. To export a FASTA file, see Create a ProSightPD database from an existing FASTA database in Proteome Discoverer.

NOTE

Be aware that FASTA files do not contain any PTM information. As such, only N-terminal modifications defined in the search nodes or modifications manually added through ProSight Annotator are considered if FASTA files are used.

Make sure the FASTA file format matches the UniProt format, particularly in the format for the file description line. Otherwise, ProSightPD might not be able to process the file.

To enable the software to process the FASTA file, edit the description line to include:

  • >sp or >tr
  • unique accession for each entry
  • pipe (|) before and after the unique accession and no spaces

This is the UniProt format:

>sp|P02144|MYG_HUMAN Myoglobin OS=Homo sapiens GN=MB PE=1 SV=2

MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH PGDFGADAQGAMNKALELFRKDMASNYKELGFQG

This is a non-conforming example:

>MYG_HUMAN

MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH PGDFGADAQGAMNKALELFRKDMASNYKELGFQG

This is an example of an acceptable user-generated FASTA file:

>sp|P02144|MYG_HUMAN

MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH PGDFGADAQGAMNKALELFRKDMASNYKELGFQG