xBobcat explained

xBobcat is a simplified version of xQuest without MS/MS information. It searches for all possible combinations of peptides that combined give rise to an indicated precursor mass. This can be helpful for very low complexity samples. Note, however, that even for small protein databases the number of possible combinations is huge and the significance for a match to a defined mass becomes low.
xBobcat digests an indicated database with the indicated enzyme settings. It allows for mixed cross-linker reactivities, mixed enzyme combinations, and one variable modification. Only few special settings are needed to start a search:
  • Enzyme settings. You can choose from a set of preselected commercially available enzymes or define your own (advanced parameters)
  • The cross-linker used with its mass. You can choose from a preselection of commercially available reagents or define your own
  • a fasta database to search (for the web version up to 50 proteins)
  • You get a xml result-file with all peptide combinations that match the precursor mass within the indicated tolerance.

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