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Oxford University Press, Plant Physiology, 1(155), p. 259-270, 2010

DOI: 10.1104/pp.110.168195

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MASCP Gator: An Aggregation Portal for the Visualization of Arabidopsis Proteomics Data

This paper is available in a repository.
This paper is available in a repository.

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Abstract

Proteomics has become a critical tool in the functional understanding of plant processes at the molecular level. Proteomics-based studies have also contributed to the ever-expanding array of data in modern biology, with many generating Web portals and online resources that contain incrementally expanding and updated information. Many of these resources reflect specialist research areas with significant and novel information that is not currently captured by centralized repositories. The Arabidopsis (Arabidopsis thaliana) community is well served by a number of online proteomics resources that hold an abundance of functional information. These sites can be difficult to locate among a multitude of online resources. Furthermore, they can be difficult to navigate in order to identify specific features of interest without significant technical knowledge. Recently, members of the Arabidopsis proteomics community involved in developing many of these resources decided to develop a summary aggregation portal that is capable of retrieving proteomics data from a series of online resources on the fly. The Web portal is known as the MASCP Gator and can be accessed at the following address: http://gator.masc-proteomics.org/. Significantly, proteomics data displayed at this site retrieve information from the data repositories upon each request. This means that information is always up to date and displays the latest data sets. The site also provides hyperlinks back to the source information hosted at each of the curated databases to facilitate more in-depth analysis of the primary data. The utilization of mass spectrometry for the characterization of proteins and biological systems has been widely embraced by plant researchers (Heazlewood and Millar, 2006; Weckwerth et al., 2008; Jorrín-Novo et al., 2009). The adoption of proteomics by the plant community can be attributed to the availability of plant genomes during the early phase of this technological development (Heazlewood and Millar, 2003). In recent years, a number of large-scale studies in the model plant Arabidopsis (Arabidopsis thaliana) have utilized proteomics and emerging technologies in mass spectrometry. These have included comparative proteomic studies (Niittylä et al., 2007; Wienkoop et al., 2008), characterization of subcellular structures within the plant cell (Heazlewood et al., 2004; Kleffmann et al., 2004; Eubel et al., 2008; Zybailov et al., 2008; Mitra et al., 2009), profiling of protein composition of plant tissues and organs (Wienkoop et al., 2004; Zou et al., 2009), examination of posttranslational modifications (Zybailov et al., 2009; Nakagami et al., 2010), and providing a genomic context to the proteome through proteogenomic mapping (Baerenfaller et al., 2008; Castellana et al., 2008). Many of these studies have resulted in large data sets comprising either protein identifications or interpreted mass spectral data. While these data sets are usually available as supplemental material or deposited into public repositories, many of these studies have led to the creation of specific online resources to facilitate further interaction with the data (Weckwerth et al., 2008). This has resulted in an increasing number of online resources where pieces of the Arabidopsis proteomic puzzle can be assembled by the informed researcher to create a picture of their protein of interest. A major problem with a centralized repository or database is its inability to respond rapidly to