A cross-linked peptide search database is written to a modified FASTA version with the .fastacp extension. Even though it is a plain text file, the database generated by Xilmass cannot be used by any other search engine. Sequence lines contain asterisks (*) and vertical bars also known as a pipe (|).

Header: Headers start with > protein accession number such as generic or [UniProtKB] (http://www.uniprot.org/) accessions are written with both start and end residue numbers of the peptide within the protein on which the enzymatic cleavage occurs (on the example, (25-37) and (11-21)). A linked-residue number on each peptide is written next (on the example, 1 and 6). The first part comes from a protein with a longer putative peptide sequence. If two peptides have the same length, the first peptide is randomly selected. In case that the entry is for mono-linked peptides, this header contains the information about the peptide and -monolinked.

Sequence: Peptide sequences are written with an asterisk (*). Two peptide sequences are separated from each other by a vertical bar (|). The first part comes from the longer putative peptide sequence. If two peptides have the same length, the first peptide is randomly selected. In case that the entry is for mono-linked peptides, this peptide contains only one peptide with an asterisk (*) that shows a linked residue.

An example for a cross-linked peptide entry:

>Q15149(25-37)_1_Q15149(11-21)_6
K*TFTKWVNKHLIK|ASEGKK*DERDR

An example for a mono-linked peptide entry:

>4Q57:B(22-27)_5-monolinked
DRVQ K*K

An example of such cross-linked peptide database can be found on here