title: DBDigger: reorganized proteomic database identification that improves flexibility and speed.
abstract: Database search identification algorithms, such as Sequest and Mascot, constitute powerful enablers for proteomic tandem mass spectrometry. We introduce DBDigger, an algorithm that reorganizes the database identification process to remove a problematic bottleneck. Typically such algorithms determine which candidate sequences can be compared to each spectrum. Instead, DBDigger determines which spectra can be compared to each candidate sequence, enabling the software to generate candidate sequences only once for each HPLC separation rather than for each spectrum. This reorganization also reduces the number of times a spectrum must be predicted for a particular candidate sequence and charge state. As a result, DBDigger can accelerate some database searches by more than an order of magnitude. In addition, the software offers features to reduce the performance degradation introduced by posttranslational modification (PTM) searching. DBDigger allows researchers to specify the sequence context in which each PTM is possible. In the case of CNBr digests, for example, modified methionine residues can be limited to occur only at the C-termini of peptides. Use of "context-dependent" PTM searching reduces the performance penalty relative to traditional PTM searching. We characterize the performance possible with DBDigger, showcasing MASPIC, a new statistical scorer. We describe the implementation of these innovations in the hope that other researchers will employ them for rapid and highly flexible proteomic database search.
authors.affiliation: Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6164, USA. tabbdl@ornl.gov
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.forename: Chandrasegaran
authors.initials: C
authors.lastname: Narasimhan
authors.forename: Michael Brad
authors.initials: MB
authors.lastname: Strader
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002851:Chromatography, High Pressure Liquid; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012269:Ribosomal Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins; D012269:Ribosomal Proteins