ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels. - Brian D. Halligan; Victor Ruotti; Weihong Jin; Scott Laffoon; Simon N. Twigger; Edward A. Dratz (Nucleic Acids Res., 2004)

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. - Brian D. Halligan; Victor Ruotti; Simon N. Twigger; Andrew S. Greene (Nucleic Acids Res., 2005)

Visualizing Quantitative Proteomics Datasets using Treemaps. - Brian D. Halligan; Shama P. Mirza; Molly C. Pellitteri-Hahn; Michael Olivier; Andrew S. Greene (IV, 2007)