image

xComb v1.3

A program that computes all possible crosslinks based on proteins of interest (Max. 30 proteins) for further interrogation using standard search engine (e.g. Phenyx, Mascot, Sequest, OMSSA, X!Tandem)


Please reference: Panchaud et al., J Proteome Res, 2010
Download xComb


News:
8th March 2012:Some modification have been added to xComb. (i) A reader for any FASTA file to accomodate any user format. (ii) Thermolysin and CNBr enzyme specificty
4th Jan 2011:A fix has been applied to xComb regarding issues with new lines with different OS formatted FASTA files. In case of strange caracters appearing (like ^M), please make sure to have your fasta file formatted in Linux (LF only for new line instead of CR LF for Dos or CR only for Mac)
Step 1: Define parameters for peptide digestion:
Type of protein sequence format: DAT format considers UniProt protein annotations (e.g. removal of methionine or signal peptide)
UniProt DAT (Flat file) UniProt FASTA Any FASTA

Enzyme specificity:

Number of missed cleavage (max = 3): This factor drastically affects the number of sequence permutations (recommended is 2)
0 1 2 3

Input: Upload your file with .dat or .fasta extension, only letters, numbers, "-", "." and "_" symbol are allowed in file name (e.g. my_file_name.dat, my_file_name.fasta)

Step 2: Define parameters for cross-linking database generation:

Type of database to be generated:
Both Intra- and Inter-protein crosslinks Only Inter-protein crosslinks Only Intra-protein crosslinks

Type of crosslinker used: Homo- or Heterobifunctional crosslinkers described by target1/target2

Specify whether amine cross-linking needs 1 trypsin missed cleavage at least: To be used with amine crosslinkers and trypsin (only peptides with at least one Lysine missed cleavage are consisered; e.g. xxxKxxxxK or xxxKxxxxR)
Off On

Specify minimum peptide length for each peptide of the pair:

Phenyx FASTA formatted output: Adds \AC= \ID= and \DE= Phenyx tags in FASTA header
Off On

Test mode which adds "|" in between peptides: For database evaluation/checking/testing purposes only (e.g. MRALPICLLALMLGGCSMLSR|QAVCIGSALNISAK)
Off On

Step 3: Download your database:
Program written by Alexandre Panchaud (University of Washington, Seattle WA)