What is it?
A program that computes all possible cross-links based on proteins of interest (Max. 30 proteins) for further interrogation using standard search engine (e.g. Phenyx, Mascot, Sequest, OMSSA, X!Tandem)
Where do I get it?
Use it online
If you are not familiar with the command line or simply don't want to fuss with installing perl (required for running this program), we provide an online interface here: Run xComb Online
xComb is one of the many software programs and tools created at the University of Washington available through our Express Licensing Program. These agreements have standard terms and conditions that allow for rapid licensing by companies, organizations, or individuals
An academic license is available to users at academic and nonprofit research institutions at no charge.
Click here --> License
For a commercial license to xComb, please contact the Express Licensing Program.
Express Licensing Program
UW Center for Commercialization
4311 11th Avenue NE, Suite 500
Seattle, WA 98105-4608
Phone: (206) 543-3970
Fax: (206) 616-3322
How do I use it?
First, you will need to install Perl. Which can be downloaded here: perl.org
Once you have Perl installed proceed with the protein2digest.pl script which takes in your fasta file(s) and produces a directory with .digest files in it.
Here is the usage protein2digest.pl ...
protein2digest.pl (version 1.3) FUNCTION: Transforms DAT or FASTA protein files into DIGEST format for further use with compatible softwares. USAGE: protein2digest.pl -in=[value] -ez=[value] -mc=[value] [file_name] -in=[value]: Specify input format 0= UniProt DAT 1= UniProt FASTA 2= Any FASTA -ez=[value]: Specify enzyme 0= Trypsin 1= Lys-C 2= Arg-C 3= Glu-C (E) 4= Glu-C (DE) 5= Asp-N 6= Trypsin, no P rule 7= ARG-C, no P rule 8= Chymotrypsin, no P rule -mc=[value]: Specify nb of missed cleavage allowed (max. = 3) [file_name]: Specify file to be converted Ex: protein2digest.pl -in=1 -ez=0 -mc=2 filename
The resulting directory can now be used by digest2cxdb.pl to create your new cross-linked database.
Here is the usage for digest2cxdb.pl ...
digest2cxdb.pl (version 1.2) FUNCTION: Creates inter & intra cross-linking databases for search with standard algorithm such as Sequest, Mascot or Phenyx. Uses pre-digested protein sequences in DIGEST format. If a single digest is present, performs only intra database. The maximum protein sequences allowed per directory in digest format is 50!!! USAGE: digest2cxdb.pl -i=[value] -x=[value] -mc=[value] -pl=[value] -f=[value] -t=[value] [digest_dir] -i=[value]: Inter/Intra type mode 0= Both intra and inter crosslinks are generated 1= Only inter crosslinks are generated 2= Only intra crosslinks are generated -x=[value]: Specify type of cross-linker 0= Amine/Amine (e.g. BS2, DST, DFDNB) 1= Sulfhydryl/Sulfhydryl (e.g. BMOE, BMDB or S-S bridge) 2= Amine/carboxyl (e.g. EDC) 3= Amine/Non-selective (e.g. SDA) 4= Amine/Sulfhydryl (e.g. AMAS, SPDP) 5= Tyrosine/Tyrosine (e.g. dityrosine) 6= Lysine/Lysine -mc=[value]: Specify whether amine cross-linking needs 1 trypsin missed cleavage at least. on=1 / off=0 -pl=[value]: Specify the minimum peptide length for building a permutation [1-6] -f=[value]: Phenyx FASTA formatted output. on=1 / off=0 -t=[value]: Test mode which adds "|" between the two peptides for easier reading. on=1 / off=0 [digest_dir]: Specifies directory containing files in DIGEST format Ex: digest2cxdb.pl -i=1 -x=1 -mc=1 -pl=4 -f=0 -t=0 digest_dir
Who do I reference if I use it?
Panchaud et al., J Proteome Res, 2010