Medicago PhosphoProtein Database
Medicago truncatula is a major model legume developed to study symbiotic associations such as legume nodulation and arbuscular mycorrhizae and also a wide variety of biological topics from plant development and pathology to evolution and ecology. We have recently utilized new tandem mass spectrometry technology to map 3,404 non-redundant sites of phosphorylation on proteins from Medicago roots (Grimsrud et al. 2010). Analysis of this data has revealed novel plant protein phosphorylation motifs and previously unreported phosphorylation sites on proteins involved in symbiotic signaling as well as many proteins with central roles in plant biology. This online database was created to provide the research community with an easy way to access legume phosphoproteomic data generated from this and future studies. When citing The Medicago Phosphoprotein Database, please reference:
Grimsrud, P. A., den Os, D., Wenger, C. D., Swaney, D. L., Schwartz, D., Sussman, M. R., Ané, J. M., and Coon, J. J. (2010) Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes, Plant Physiology, 152, 19-28.
Sample Information: The data presented here represents a large-scale shotgun mass spectrometry analysis of peptides derived from Medicago root proteins. The seedlings were placed on an aeroponic system and grown in nitrogen-free modified Fahraeus medium for 14 to 15 d at 22 degrees C and 24 h of 130 to 200 umol m-2 s-1 light. The roots, however, grew in the dark. Proteins were isolated using a chloroform/methonol precipitation, digested with Trypsin, LysC, AspN, or GluC, and sequenced using an LTQ Orbitrap XL employing either ETD or CAD fragmentation.
Using the Database:
- Search Type: To perform a search select “Search” under the “Tools” menu. Choose the desired search type under “Search Options” to perform a search in one of the three following ways:
- Description: Enter a name, accession number, or functional description term for a protein of interest in the “Search Terms”.
- Blast: Enter a sequence of interest in the “Search Terms” and select an E-value threshold.
- Amino Acid Sequence / Phosphorylation Motif: Enter part of or the entire sequence for a protein of interest. There is no length minimum or maximum, as the search is not limited to the phosphopeptide identified, but considers all regions of the proteins to which the identified phosphopeptides map. Entering a lower-case “s”, “t”, or “y” specifies phosphorylation. An “x” indicates any amino acid and a “*”indicates any string of amino acids.
- Search Results: After clicking “Search” button, the entire sequences of proteins (or parsimonious protein groups identified by identical peptides) matching the search criteria will be displayed. All sites of phosphorylation will be indicated by a lower-case “s”, “t”, or “y”. Underlined green lettering indicates localized sites of phosphorylation, from phosphopeptides in which the exact amino acid residue of the phosphoryl modification could be determined from the MS data. Red lettering without underlining indicates non-localized (potential) sites of phosphorylation from ambiguous positional isomers. Clicking on either a localized or non-localized site of phosphorylation will bring up a summary of the pertinent tandem MS data from all the scans leading to the identification of that site of phosphorylation, as well as a reference of the publication reporting this data.
- Browse: Scroll through our database page-by-page.
- Download: Download all protein sequences with phosphorylation sites indicated to browse through our entire database as an excel file.
Other Plant Databases:
The inception of large scale proteome profiling techniques has prompted the creation of databases dedicated to the storage and dissemination of information relating to various species. Below we link a subset of databases related to plant proteomics of both multiple and single plant species.
- ProMEX: Promex is a mass spectral reference database consisting of tryptic peptide fragmentation mass spectra derived from plants.
- P3DB: Protein phosphorylation data for 6 species from 23 experimental studies, containing 11,601 phosphoproteins, harboring 32, 963 phosphosites.
- PhosPhAt: The Arabidopsis protein phosphorylation site database, contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups.
- GelMap: Gelmap is a universal tool for spot visualization on a gel image. The group that drives the development of this project analyzes the major aspects of plant proteomics.
- PPDB: The Plant Protein Database (PPDB) holds Arabidopsis and maize experimental data from in house proteome and mass spectrometry analysis, curated information, about protein function, protein properties, and subcellular localization.
- MASCP: Multinational Arabidopsis steering committee was established to facilatate the coordination of international research in Arabidopsis thaliana in the area of proteomics.
- Soybean Proteome Database: Based on data of soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE).
- Rice Proeome Database: Proteome data derived from 2D-PAGE gels from several tissues and organelles.