ProFound: an expert system for protein identification using mass spectrometric peptide mapping information.

By Wenzhu Zhang, Brian T. Chait. Analytical Chemistry, 2000

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SIRIUS: decomposing isotope patterns for metabolite identification (2008, background): “Zhang and Chait (2000) and Zhang et al. (2002) suggest to use Bayesian Statistics to evaluate mass spectra matches: P(Mj|D,B)= P(Mj|B) ·P(D|Mj,B)∑ i P(Mi|B)P(D|Mi,B) , (4) where D is the data (the measured spectrum), Mi are the models (the candidate molecules) and B stands for any prior background…”
Molecular Biologist's Guide to Proteomics (2002, methodology): “Search programs used for peptide mass fingerprinting include PepSea (102), PeptIdent/MultiIdent (165), MS-Fit (32), MOWSE (125), and ProFound (176).”
Proteomic analysis of the mammalian nuclear pore complex (2002, methodology): “Peptide mapping data obtained by MALDI-QqTOF-MS were compared with theoretical maps computed from protein sequences present in the NCBI nonredundant (NR) database, using the program ProFound (Zhang and Chait, 2000).”