title: Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.
abstract: The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors: Eric W
authors: EW
authors: Deutsch
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors: Zhi
authors: Z
authors: Sun
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors: David S
authors: DS
authors: Campbell
authors: CHUV Centre Universitaire Hospitalier Vaudois , 1011 Lausanne, Switzerland.
authors: Pierre-Alain
authors: PA
authors: Binz
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors: Terry
authors: T
authors: Farrah
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors: David
authors: D
authors: Shteynberg
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors: Luis
authors: L
authors: Mendoza
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.|Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan , Ann Arbor, Michigan 48109, United States.
authors: Gilbert S
authors: GS
authors: Omenn
authors: Institute for Systems Biology , Seattle, Washington 98109, United States.
authors: Robert L
authors: RL
authors: Moritz
mesh_terms: D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein / Q000639:trends*; D006367:HeLa Cells; D006801:Humans; D008099:Liver / Q000737:chemistry / Q000166:cytology; D013058:Mass Spectrometry; D020033:Protein Isoforms / Q000032:analysis; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*
chemical_list: D020033:Protein Isoforms; D011506:Proteins
keywords: human; search databases; shotgun mass spectrometry