Frequently asked questions

Video tutorial

1. What operating system supports XLink-DB?


XLink-DB runs on both windows and OS X, but it will not work on linux because the java plugin for web browser is lacking.

2. What web browsers should I use?


XLink-DB runs nicely on latest Firefox, Safari and Chrome. IE is not recommended because the script runs a bit slowly.

3. Does it matter what cross-linker I used to generate data?


No. The data input is independent of what cross-linker you used to generate data.

4. What organisms does XLink-DB support?


E.coli and H.sapiens. More organisms will be incorporated into XLink-DB later.

5. What input file format should I use?


A tab delimited text file. Arrange the columns as "Peptide A / Protein A / Labeled position A / Peptide B / Protein B / Labeled position B".

Please use UniProt ID as protein identifier. The labeled position means the position of the labeled site on the peptide, start from 0. Please do not use table header.

A template file is available in the download page for your reference.

6. What should I do if I found a bug or I got a brilliant suggestion?


Join us in our google discussion group

7. What reference protein interaction database is XLink-DB using?


Primarily, XLink-DB is using data from IntAct. For E.coli, EciD is used instead.