Goals

From Mascp

Jump to: navigation, search

Goals supporting the Arabidopsis 2021 Roadmap: From bench to a bountiful harvest

A) Build a predictive model of an Arabidopsis plant from its molecular parts

  • Build on large scale proteogenomic mapping efforts and integrative subcellular profiling to further enhance and expand current whole plant and subcellular protein expression maps in Arabidopsis
  • Create a resource of validated Arabidopsis proteotypic peptides that can be employed for SRM-based quantitative analyses of proteins by mass spectrometry (e.g. AtSRM Atlas)
  • Continue to expand and integrate new proteomics resources through the MASCP Gator


B) Exploit the wealth of natural variation that exists in Arabidopsis to further our understanding of adaptation and evolution

  • Construct a 1001 proteomes portal for community exploitation and visualization of proteomes from Arabidopsis natural variants
  • Undertake a coordinated proteomic analysis of Arabidopsis accessions to both validate genomics data and to identify specific SRM markers (based on nsSNPs) for specific proteins from accessions for future quantitative analyses


C) Establish an effective knowledge exchange pipeline from the laboratory to the field and vice versa

  • Assist in the coordination proteomics activities in other plant systems through representations as the Arabidopsis committee on the International Plant Proteomics Organization (INPPO)
  • Actively pursue proteomics research programs in other plant systems using key knowledge gained through the analysis of Arabidopsis


D) Build the International Arabidopsis Informatics Consortium (IAIC), an international informatics and data infrastructure

  • Maintain and enhance existing informatics infrastructure in Arabidopsis proteomics
  • Create new resources to exploit emerging technologies (e.g. AtSRM Atlas)
  • Develop international proteomics standards in coordination with the iMOP program
  • Continue to coordinate the integration of Arabidopsis proteomics resources through the MASCP Gator
  • Integrate proteomics data resources with other informatics resources in Arabidopsis


E) Deepen International Cooperation and Coordination

  • Represent Arabidopsis proteomics activities and develop proteomics standards through interactions with the initiative on Model Organism Proteomes program (iMOP) as part of the Human Proteome Organization (HUPO)
  • Represent Arabidopsis proteomics interests as representatives of the International Plant Proteomics Organization (INPPO)
  • Continue to offer proteomics workshops at international conferences

Goals supporting the Arabidopsis 2010 Functional Genomics Program

1. Work towards a central international database of MS/ MS spectra derived from Arabidopsis samples.

  • With the development and release of the MASCP Gator, a web portal that aggregates proteomics data from a variety of community based Arabidopsis proteomic resources, this goal has been accomplished. Will endeavor to integrate emerging databases and resources with the MASCP Gator as they become available.

Responsible MASCP Members: Joshua Heazlewood, Wolfram Weckwerth

2. Establishment of a high density proteome map of Arabidopsis thaliana using different tissues and high throughput mass spectrometry as a basis for future systems biology approaches.

  • With the release in 2008 of large-scale Arabidopsis proteomics sets comprising multiple organ analysis (AtProteome and AtPeptide) and in conjunction with the proteo-genomic visualization tools and analysis, aspects of this objective have been completed. These data have also been made available at TAIR as tracks on the Arabidopsis genome browser. Some aspects of this work was recently updated with a new proteomic analysis of Arabidopsis organs and tissues and includes global protein quantitation by spectral counts (pep2pro).

Responsible MASCP Members: Steve Briggs, Katja Baerenfaller, Sacha Baginsky

3. Discuss international network grant proposals for plant proteomics.

  • The European COST action FA 0603 Plant Proteomics initiated some networking between proteomics researchers within Europe.

Responsible MASCP Members: Wolfram Weckwerth

4. Develop standards for two-dimensional gel-electrophoresis, shotgun proteomics, and quantitative proteomics.

Responsible MASCP Members: Joshua Heazlewood, Katja Baerenfaller

  • MASCP recently joined the Human Proteome Organizations iMOP initiativeto represent Arabidopsis coordinate the development of proteomic standards in model systems.

Responsible MASCP Members: Steve Briggs, Klaas van Wijk, Katja Baerenfaller, Alexandra Jones

5. Write guidelines for minimum requirements for different types of proteomic studies and distribute these to plant journals (specifically: Plant Molecular Biology, Plant Physiology, The Plant Cell, and The Plant Journal) for their consideration of publication standards—issues include experimental method, data analysis and call of identifications.

6. Collaborate with other interested parties on Arabidopsis proteomic data storage.

  • MASCP encourages and has made recommendations for the storage of raw data from proteomics experiments (published or unpublished.

Responsible MASCP Members: Katja Baerenfaller

  • We have initiated a proposal to formalize and develop a closer integration of Arabidopsis proteomics data storage through PRIDE and live visualization through the MASCP Gator.

Responsible MASCP Members: Alex Jones

7. Seek funding opportunities for the exchange of students and young researchers between different labs in order to develop a common training initiative.

  • We have expanded the Funding section to include information on international fellowships that are available to early career researchers. Since 2004 we have actively sought to organize proteomics workshops at international meetings and conferences.

Responsible MASCP Members: Joshua Heazlewood

Retrieved from "http://www.masc-proteomics.org/mascp/index.php/Goals"