Parameter: cross_link

Overview

Specifies the sites of cross-linking and mass modification. Four values follow this parameter, separated by spaces. The first two values are one or more amino acid letters (uppercase only) that can be linked. These can be the same or different depending on whether the cross-linker is homobifunctional or heterobifunctional. Use lowercase ‘n’ or ‘c’ if the linker can bind the protein termini. The third value is the net mass value of the cross-linker when bound to the peptides. The mass can be any real number, positive or negative. The identifier is any name desired for the cross-linker. If the data contain multiple cross-linkers, use multiple cross_link lines in the configuration file, one for each cross-linker used.

Syntax

[Amino Acid(s)] [Amino Acid(s)] [Mass] [Identifier]

Version

1.5.0 - present

Example

cross_link  =  nK  nK  138.0680742  BS3

Deprecated Syntax for versions 1.0 - 1.4.3

[Chem Code] [Chem Code] [Mass]

Chem Codes

• 1 = amine (K or n-terminus)
• 2 = carboxyl (D, E, or c-terminus)
• 3 = sulfhydryl (C)
• 4 = acyl (Q)