crux search-for-xlinks [options] <ms2 file> <protein fasta file> <link sites> <link mass>


This command compares a set of spectra to cross-linked peptides derived from a protein database in FASTA format. For each spectrum, the program generates a list of candidate molecules, including linear peptides, dead-end products, self-loop products and cross-linked products, with masses that lie within a specified range of the spectrum's precursor mass. These candidate molecules are ranked using XCorr, and the XCorr scores are assigned statistical confidence estimates using an empirical curve fitting procedure.

The algorithm is described in more detail in the following article:

Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. Goodlett and William Stafford Noble. "Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs." Journal of Proteome Research. 2010.

In search-for-xlinks, properties of the cross-linker are specified using the two required command line arguments, and . In addition, mass shifts associated with mono-links can be specified using the --mod option. Below are suggested parameter settings for some commonly used cross-linkers:

Linker Link Mass Link Sites Mono Link
EDC -18.0156 K:D,E,cterm  
BS2 96.0211296 K,nterm:K,nterm --mod 114.0316942,113.0476524:K,nterm:1:T:T
BS3 138.0680742 K,nterm:K,nterm --mod 156.0786,155.0946278:K,nterm:1:T:T
DSS 138.0680796 K,nterm:K,nterm --mod 156.0786,155.0946278:K,nterm:1:T:T
AMAS 137.011 K,nterm:C --mod 155.02156:K,nterm,C:1:T:T
GMBS 165.0422 K,nterm:C --mod 183.05276:K,nterm,C:1:T:T
formaldehyde 9.98435 K,W,nterm:H,N,Y,K,W,R,nterm --mod 12.0,30.010565:K,W,nterm:1:T:T



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: