Parameter: search_dimers


DEPRECATED This parameter has been deprecated and is ignored in the current release of Kojak.

Some highly purified and concentrated samples display electrospray artifacts such as non-covalent dimerization of non-linked peptides. These non-covalent dimers appear in MS/MS spectra as two peptide fragment ion series with a precursor mass equal to the non-linked sum of the two constituent peptide masses. Depending on sample preparation, these dimers can be prevalent and require searching, although at a computational expense.

Setting this parameter to 1 turns on searches for non-covalently linked dimers (not cross-links). This will no worse than double search time and is only recommended for highly concentrated and purified samples.




1.0 - 1.4.1 DEPRECATED


search_dimers = 1