RESUMO
LC MS/MS has become an established technology in proteomic studies, and with the maturation of the technology the bottleneck has shifted from data generation to data validation and mining. To address this bottleneck we developed Experimental Peptide Identification Repository (EPIR), which is an integrated software platform for storage, validation, and mining of LC MS/MS-derived peptide evidence. EPIR is a cumulative data repository where precursor ions are linked to peptide assignments and protein associations returned by a search engine (e.g. Mascot, Sequest, or PepSea). Any number of datasets can be parsed into EPIR and subsequently validated and mined using a set of software modules that overlay the database. These include a peptide validation module, a protein grouping module, a generic module for extracting quantitative data, a comparative module, and additional modules for extracting statistical information. In the present study, the utility of EPIR and associated software tools is demonstrated on LC MS/MS data derived from a set of model proteins and complex protein mixtures derived from MCF-7 breast cancer cells. Emphasis is placed on the key strengths of EPIR, including the ability to validate and mine multiple combined datasets, and presentation of protein-level evidence in concise, nonredundant protein groups that are based on shared peptide evidence.
Assuntos
Cromatografia Líquida/métodos , Bases de Dados Factuais , Armazenamento e Recuperação da Informação , Espectrometria de Massas/métodos , Peptídeos/análise , Reprodutibilidade dos Testes , Neoplasias da Mama/química , Gráficos por Computador , Sistemas de Gerenciamento de Base de Dados , Feminino , Humanos , Peptídeos/química , Projetos de Pesquisa , Software , Células Tumorais CultivadasRESUMO
This paper describes a way of including entry ramps in the Nagel-Schreckenberg traffic model. The idea is to place what are called shadow cars on a highway next to cars on entry ramps, which enables the drivers to take ramp cars into account. The model is shown to capture important real-life traffic phenomena that have not been included in previous models. Furthermore, it is demonstrated that the desirable properties of the Nagel-Schreckenberg model are retained.