crux bullseye [options] <MS1 spectra> <MS2 spectra>


Bullseye assigns high resolution precursor m/z values to fragmentation (MS2) spectra. Bullseye uses the Hardklör algorithm to identify persistent isotope distributions (PPIDs) in precursor (MS1) scans. For each PPID, MS2 scans that occur within a specified time and m/z range are assigned the average monoisotopic m/z from the PPID assigned as the precursor m/z. A detailed description of the Bullseye algorithm is given in

Hsieh EJ, Hoopmann MR, Maclean B, MacCoss MJ. "Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data". Journal of Proteome Research. 9(2):1138-43, 2010.

Note that, in complex samples, it is not unusual for multiple PPIDs to be found near an MS2 spectrum. In those cases, Bullseye will assign both mass measurements to the spectrum. In a .ms2 file, multiple Z line entries will be made for the scan number.

It is possible to reduce the number of scans that receive multiple PPIDs by adjusting Bullseye's parameters. For example, reducing the retention time tolerance ("--retention-tolerance") or reducing the tolerance for persistent peptides ("--persist-tolerance") will reduce the chances of multiple PPIDs being assigned.

Bullseye uses Hardklör, so all of the Hardklör parameters may also be used with Bullseye. For users familiar with the standalone version of Bullseye, the parameter mapping is here.



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: