The Goodlett Laboratory

xComb v1.3

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

Licensing Information

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

Academic License

An academic license is available to users at academic and nonprofit research institutions at no charge.
Click here --> License

Commercial 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
Email: license@u.washington.edu

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