title: Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets.
abstract: Dependent on concise, predefined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference databases. However, such algorithms have been difficult to apply to complex protein mixtures, in part due to a lack of methods for automatically validating de novo sequencing results. Here, we present novel metrics for benchmarking de novo sequencing algorithm performance on large-scale proteomics data sets and present a method for accurately calibrating false discovery rates on de novo results. We also present a novel algorithm (LADS) that leverages experimentally disambiguated fragmentation spectra to boost sequencing accuracy and sensitivity. LADS improves sequencing accuracy on longer peptides relative to that of other algorithms and improves discriminability of correct and incorrect sequences. Using these advancements, we demonstrate accurate de novo identification of peptide sequences not identifiable using database search-based approaches.
authors.affiliation: Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States.
authors.forename: Arun
authors.initials: A
authors.lastname: Devabhaktuni
authors.affiliation: Department of Chemical & Systems Biology, Stanford University , Stanford, California 94035, United States.
authors.forename: Joshua E
authors.initials: JE
authors.lastname: Elias
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D010455:Peptides / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods* / Q000592:standards; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides
keywords: MS/MS; de novo peptide sequencing; large-scale computational analysis; mass spectrometry; proteomics