The PROTICdb database for 2-DE proteomics.

@article{Langella2007ThePD,
  title={The PROTICdb database for 2-DE proteomics.},
  author={Olivier Langella and Michel Zivy and Johann Joets},
  journal={Methods in molecular biology},
  year={2007},
  volume={355},
  pages={
          279-303
        }
}
PROTICdb is a web-based database mainly designed to store and analyze plant proteome data obtained by 2D polyacrylamide gel electrophoresis (2D PAGE) and mass spectrometry (MS). The goals of PROTICdb are (1) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements; and (2) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data… 
View on PubMed
doi.org
16 Citations
Background Citations
1
Methods Citations
6

16 Citations

Citation Type

Citation Type

Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction
TLDR
This work presents here an evolution of PROTICdb, a database software that now handles MS data, including quantification, and provides means for data storage, enrichment, and dissemination of proteomics data.
Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus
TLDR
Comparative proteomics was applied to three vegetative organs of Brassica napus, the leaf, stem, and root using 2‐DE, suggesting the existence of a “basal” or ubiquitous proteome composed of housekeeping proteins.
Transcriptomic and proteomic data in developing tomato fruit
An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato.
Information management for proteomics: a perspective
TLDR
A perspective on data management in proteomics is provided and the implications for academic and industry-based researchers working in this field are provided.
Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance
TLDR
This study evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds and compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance.
Using SCDL for Integrating Tools and Data for Complex Biomedical Applications
TLDR
The BioSemantic System is presented to bridge complex biological/biomedical research problems and computational solutions via semantic computing and presents an algorithm to map a user request to one or more existing services if they exist.
A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast*
TLDR
It is shown that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered, and this proportion was higher at nonoptimal temperature for intraspecific hybrids than for interspecific hybrids.
Peptide filtering differently affects the performances of XIC-based quantification methods.
Yeast proteome variations reveal different adaptive responses to grape must fermentation.
TLDR
The results indicate that the ability of S. cerevisae and S. uvarum to complete grape must fermentation arose through different evolutionary roads, involving different metabolic pathways and duplicated genes.
...
1
2
...

References

SHOWING 1-5 OF 5 REFERENCES
PROTICdb: A web‐based application to store, track, query, and compare plant proteome data
PROTICdb is a web‐based application, mainly designed to store and analyze plant proteome data obtained by two‐dimensional polyacrylamide gel electrophoresis (2‐D PAGE) and mass spectrometry (MS). The…
Proteomics to study genes and genomes
TLDR
Proteomics can be divided into three main areas: protein micro-characterization for large-scale identification of proteins and their post-translational modifications; ‘differential display’ proteomics for comparison of protein levels with potential application in a wide range of diseases; and studies of protein–protein interactions using techniques such as mass spectrometry or the yeast two-hybrid system.
Current two‐dimensional electrophoresis technology for proteomics
TLDR
The current 2‐DE/MS workflow is described including the following topics: sample preparation, protein solubilization, and prefractionation; protein separation by 1‐DE with IPGs; protein detection and quantitation; computer assisted analysis of 2-DE patterns; protein identification and characterization by MS; two‐dimensional protein databases.
Plant proteome analysis
TLDR
An overview is given on proteome studies performed to analyze whole plants or specific tissues with particular emphasis on important physiological processes such as germination and the use of proteome approaches to investigate the interaction of plants with pathogens or with symbiotic organisms.
Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource
TLDR
The Gene Ontology (GO) project provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences.