PepNovo: de novo peptide sequencing via probabilistic network modeling.

By Ari Frank, Pavel A. Pevzner. Analytical Chemistry, 2005

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A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, neutral): “com/Lutefisk b PepNovo [270] proteomics.”
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2011, methodology): “Representative de novo sequencing software packages include PEAKS (1), PepNovo (2), NovoHMM (3), and Lutefisk (4), and representative database search software packages include Mascot (5), SEQUEST (6), X!Tandem (7), OMSSA (8), ProteinProspector (9), MaxQuant”
De novo peptide sequencing by deep learning (2017, methodology): “These measures of sequencing accuracy have been widely used in previous publications (10, 12, 19).”
Spectral Probabilities and Generating Functions of Tandem Mass Spectra: a Strike Against Decoy Databases (2008, background): “30,32,40 This transformation takes into account peptide length, peak intensities, neutral losses, dependencies between ion types, noise, and so forth.”
ProLuCID: an improved SEQUEST-like algorithm with enhanced sensitivity and specificity (2015, background): “…unambiguous “ peptide sequence tags ” derived from spectra that are used to search known sequences [11 – 15] (3) peptide de novo sequencing [16 – 24], (4) probability-based matching that calculates a score based on the statistical signi ﬁ cance of a match between an observed peptide fragment…”