MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data

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.

Figure 1.

Schematic diagram of the retrieval processes for the MASCP Gator. Data are requested from the various proteomic resources via an API and passed to the data adaptors that can each understand the data and populate the appropriate parts of the MASCP Gator for visualization. A total of nine resources (AtPeptide, AtProteome, SUBA, TAIR, PhosPhAt, PPDB, ProMEX, RIPP-DB, and AT_CHLORO) are integrated into the MASCP Gator, with the AT_CHLORO service currently under development.

Figure 2.

Screenshot of the MASCP Gator interface and result output. The interface was created to be visually intuitive with all necessary information available at a glance. A user simply enters an AGI into the field at the top of the page and clicks the “Retrieve” button (or ENTER). The multiple AGI retrieval facility is accessible through the “Advanced” button. A, Protein sequence is represented as a scale bar. B, Peptides from various data sources are displayed as colored lines with a hydropathy plot shown underneath. C, The control panel provides access to extra features. D, Subcellular information and mass spectral source organ evidence are shown as tag clouds to provide weighted abundance information. “Fluorescent protein” indicates localization by a fluorescent protein, “Proteomic” indicates localization by proteomics, and “Predicted” indicates the predicted subcellular localization. Green and red markers at the bottom of the page indicate whether communication with the external resource was successful.

Figure 3.

A detailed view of the MASCP Gator interface. The zoom and pan features allow full peptide-to-protein context and can display the precise location of any known modifications in the amino acid sequence. This view also clearly shows overlapping peptide information and can be used to identify modulated modification sites and reliable and compatible peptide tags for mass spectrometry-based quantitative studies such as selected reaction monitoring in a triple quadrupole mass spectrometer. [See online article for color version of this figure.]