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xComb

What is xComb?

xComb is 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). If you use xComb, please cite our original publication:

Panchaud A, Singh P, Shaffer S a, Goodlett DR. xComb: A Cross-Linked Peptide Database Approach to Protein-Protein Interaction Analysis. J Proteome Res 2010;9:2508–15. [Link]

Licensing Information

xComb is available as open source software here on GitHub, under the GNU General Public License Version 3.0 (See the LICENSE.md file for details). Though we offer xComb free for non-profit and academic use, commercial interests should be directed through the Unversity of Washington Express Licensing Program at:

UW CoMotion
4545 Roosevelt Way NE, Suite 400
Seattle, WA 98105
Phone: (206) 543-3970
Fax: (206) 616-3322
Email: license@uw.edu

How do I use it? (2 options)

1. On the web

The easiest way to use xComb is through our website.

2. Download and use the software locally

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.

Below is an example of the usage for protein2digest.pl:

protein2digest.pl (xComb v1.4)

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
                9= Thermolysin

        -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.

Below is an example of the usage for digest2cxdb.pl:

digest2cxdb.pl (xComb v1.4)

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

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A Cross-Linked Peptide Database Approach to Protein−Protein Interaction Analysis

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