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YPED specifications

Information


Unique identifier OMICS_20682
Name YPED
Alternative name Yale Protein Expression Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Mark Shifman
  • person_outline YPED Team

Publication for Yale Protein Expression Database

YPED citations

 (4)
library_books

YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry based Proteomics Research

2015
PMCID: 4411476
PMID: 25712262
DOI: 10.1016/j.gpb.2014.11.002

[…] geneous sources. This makes data comparison and integration difficult across proteomics experiments conducted independently by different research groups. To address issues such as these, we developed Yale Protein Expression Database (YPED; version 1.0) as a uniform system for collecting proteomic data derived from multiple samples that have been submitted by hundreds of investigators for analysis […]

library_books

Revealing the amino acid composition of proteins within an expanded genetic code

2014
Nucleic Acids Res
PMCID: 4333366
PMID: 25378305
DOI: 10.1093/nar/gku1087

[…] l tryptic peptides reporting UAG suppression in any of the 328 UAG containing ORF's. Differences of ORFs reported by Lajoie () and our database are listed in Supplementary Table S10. PSM deposited in Yale Protein Expression Database (YPED) were then matched with a custom Java routine using the regular expression functions to generate a customizable text file with all matching identified peptides. […]

library_books

Exploring the Nicotinic Acetylcholine Receptor associated Proteome with iTRAQ and Transgenic Mice

2013
PMCID: 3806329
PMID: 23891776
DOI: 10.1016/j.gpb.2013.05.005

[…] th hybrid sequence tag and feature probability database searches . Hence, specific details such as mass tolerances, specific modifications, etc. are not used. All iTRAQ results were uploaded into the Yale protein expression database (YPED; http://yped.med.yale.edu/repository/) . […]

library_books

iQuantitator: A tool for protein expression inference using iTRAQ

2009
BMC Bioinformatics
PMCID: 2770557
PMID: 19835628
DOI: 10.1186/1471-2105-10-342

[…] ware package for iTRAQ data analysis, provides protein-level relative expression estimates and associated uncertainty measures using error propagation techniques []. Data management tools such as the Yale Protein Expression Database (YPED) facilitate biological interpretation through the capture, display, and linking of data from proteomic experiments using a variety of experimental techniques inc […]

Citations

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YPED institution(s)
Center for Medical Informatics, Department of Anesthesiology, Keck Biotechnology Resource Laboratory, Department of Genetics, Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry, and Department of Computer Science, Yale University, New Haven, CT, USA
YPED funding source(s)
Supported by Federal funds from NIH/NHLBI contract N01-HV-28186 and NIH/NIDA grant P30 DA018343.

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