title: MScDB: a mass spectrometry-centric protein sequence database for proteomics.
abstract: Protein sequence databases are indispensable tools for life science research including mass spectrometry (MS)-based proteomics. In current database construction processes, sequence similarity clustering is used to reduce redundancies in the source data. Albeit powerful, it ignores the peptide-centric nature of proteomic data and the fact that MS is able to distinguish similar sequences. Therefore, we introduce an approach that structures the protein sequence space at the peptide level using theoretical and empirical information from large-scale proteomic data to generate a mass spectrometry-centric protein sequence database (MScDB). The core modules of MScDB are an in-silico proteolytic digest and a peptide-centric clustering algorithm that groups protein sequences that are indistinguishable by mass spectrometry. Analysis of various MScDB uses cases against five complex human proteomes, resulting in 69 peptide identifications not present in UniProtKB as well as 79 putative single amino acid polymorphisms. MScDB retains ~99% of the identifications in comparison to common databases despite a 3-48% increase in the theoretical peptide search space (but comparable protein sequence space). In addition, MScDB enables cross-species applications such as human/mouse graft models, and our results suggest that the uncertainty in protein assignments to one species can be smaller than 20%.
authors.affiliation: Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany.
authors.forename: Harald
authors.initials: H
authors.lastname: Marx
authors.forename: Simone
authors.initials: S
authors.lastname: Lemeer
authors.forename: Susan
authors.initials: S
authors.lastname: Klaeger
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.forename: Bernhard
authors.initials: B
authors.lastname: Kuster
mesh_terms: D000465:Algorithms; D000818:Animals; D045744:Cell Line, Tumor; D030562:Databases, Protein; D005260:Female; D006801:Humans; D013058:Mass Spectrometry; D051379:Mice; D010446:Peptide Fragments / Q000032:analysis*; D010920:Placenta / Q000737:chemistry / Q000166:cytology; D011110:Polymorphism, Genetic; D011247:Pregnancy; D011506:Proteins / Q000737:chemistry*; D059748:Proteolysis; D040901:Proteomics / Q000379:methods*; D012984:Software; D013045:Species Specificity
chemical_list: D010446:Peptide Fragments; D011506:Proteins