YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.
Genomics Proteomics Bioinformatics
; 13(1): 25-35, 2015 Feb.
Article
en En
| MEDLINE
| ID: mdl-25712262
ABSTRACT
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Fragmentos de Péptidos
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Cromatografía Liquida
/
Biología Computacional
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Proteoma
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Bases de Datos de Proteínas
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Proteómica
/
Espectrometría de Masas en Tándem
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
Genomics Proteomics Bioinformatics
Asunto de la revista:
BIOQUIMICA
/
GENETICA
/
INFORMATICA MEDICA
Año:
2015
Tipo del documento:
Article