FASTA files are just text files, so you can open them up in your favorite text editor to see what they look like. The file you linked has a single entry. The first line begins with
> and contains information about the sequence, delimited by
| characters – the accession number, chain info, gene name, species, etc. Subsequent lines are just the protein sequence using the standard 20-letter alphabet for amino acids, or the nucleotide sequence from 5'-3' using ACTG. There can be multiple entries in a file, delineated by one or more blank lines.
If for whatever reason your instrument or vendor won't accept FASTA files, a very simple low-throughput solution is to just delete the first line of single-entry files, or delete any lines beginning with
> for multiple-entry files. If you have many files to process, this can be automated using Unix/Linux command line tools or a scripting language like Python or Perl.