The following tools can be used with the 4700/4800 MALDI TOF/TOF mass spectrometers. If you have any questions, please contact me at <bryanesmith at gmail.com>.
Very easy-to-use object-oriented Java API for connecting to the mass spectrometer remotely and extracting monoisotopic peak lists. Useful if want to make an application that extracts the peak lists directly from the instrument instead of having to download the files manually.
Uses T2Util to get information from specified instrument (using IP address). Using MS peak list, looks for peaks of specified mass difference (e.g., 112 Da) to infer potential crosslink candidates. Outputs an inclusion list than can be used to run MS-MS. This is not a cross-linked peptide validation tool, but rather a way to find potential crosslink candidates.
Optionally specify required intensity or spot windows (i.e., number of consecutive spots from which to include the most intense peak pairs if same masses).
There is a simple Java API as well as a GUI written in JavaFX.
You can launch the tool using Java Web Start: http://www.proteomecommons.org/dev/XLinkCandidate/run-gui.jnlp