Proteome Maps: New Possibilities for Web-based Annotation of Proteome Data
- Fig. 1: Features of GelMap: (i) Assigment of any number of identified proteins per "spot", (ii) Functional annotation of all identified proteins, (iii) Direct access to compact information as well as links to detailed additional information.
- Fig. 2: Filter options in GelMap: (i) by name, (ii) by "accession" number, (iii) by numbering on a two-dimensional gel.
- Fig. 3: Workflow for the production of a proteome map with GelMap: (i) Creation of primary data (two-dimensional protein gel, identification of proteins by mass spectrometry), (ii) Processing of the primary data with suitable software packages, (iii) Production of the GelMap.
- Prof. Dr. Hans-Peter Braun, Director, Institute of Plant Genetics, Leibniz University Hannover
- Michael Senkler, Software Developer, Institute of Plant Genetics, Leibniz University Hannover
Proteome analysis is one of the most important methods for the investigation of vital processes. Up to now, this has been based primarily on protein separation by means of gel electrophoresis with subsequent identification of the proteins by mass spectrometry. Here, we present a new platform, „GelMap" (http://www.gelmap.de/), for the web-based annotation of proteome data.
Since the completion of the first genome sequencing projects it is known that higher forms of life have between 10,000 and 50,000 different genes. On the basis of the „one gene, one polypeptide" hypothesis, a corresponding number of proteins is expected. However, in the meantime it has been discovered that due to genetic mechanisms and protein modification processes, the number of different protein types in higher forms of life is considerably higher. How can a variety of substances of this magnitude be analysed by protein biochemistry?
A traditional, and up to now widespread method is two-dimensional polyacrylamide gel electrophoresis (2D PAGE). Here, proteins are initially separated in a first gel dimension by means of „iso-electric focussing" (IEF). Subsequently, separation of the proteins according to their molecular masses is performed in the orthogonal direction. By means of this method, up to 10,000 different proteins can be separated .
For only 10 years, more powerful methods for the systematic identification of proteins separated by gel electrophoresis have been available. These are usually based on mass spectrometry methods. The end products of a typical proteome analysis are therefore (a) the image of two-dimensional protein gels and (b) long lists with identified proteins, which are assigned to the protein „spots" on the gels by means of numbers and arrows.
Publication of Proteome Data
How can these complex results be published efficiently? Originally, all primary proteomic data were published in original scientific articles. However, the lists of the identified proteins are becoming increasingly extensive, so that nowadays, the primary data are increasingly being published in the form of supplementary material, which can be viewed on the websites of specialist journals.
As an alternative, the web based annotation of proteome data has recently become established.
Here, the protein spots on two-dimensional images are directly linked to information about the relevant proteins. Many work groups now provide protein reference maps in the form of linked gel images on their websites. In addition, web portals have been established, via which the protein reference maps are internationally linked, e.g. „World 2D PAGE" (http://world-2dpage.expasy.org/list/). However, the previously available software programs for the production of proteome reference maps have left much to be desired.
Web-based Presentation of Proteome Data with GelMap
GelMap is a new program for the annotation of original proteomic data . The production of a reference map can be simply performed in a browser, without technical preparations. In comparison with previously available software packages, GelMap offers many additional possibilities (fig. 1): (i) Several proteins can be linked to the individual protein spots. This is important insofar as due to superimposition effects on the protein gels, in almost all cases, more than one protein can be detected for each spot. With the aid of GelMap a complete annotation of MS data is now possible for the first time. (ii) All proteins are functionally annotated on up to three levels. For example, metabolic areas, metabolic paths or protein complexes can be defined as functional categories. With the aid of a side menu, the functional categories can be called up and corresponding proteins visualized on the gel image. (iii) Comprehensive information about all proteins is provided by clicking on the spots. This is done in the form of compact information in a small frame, via which access is provided to detailed information in two tables in the background (hyperlinks „more protein details", „more peptide details") as well as to external databases. In addition, the platform provides extensive search options with auto-completion, in order to simply and rapidly find proteins according to their names, accession codes or numbers (fig. 2). Furthermore, there are automated access facilities via a programming interface („API") in order to make the available data accessible, e.g. in meta-search engines.
The possibilities of the platform are best revealed by „visiting" reference maps which have already been produced. In the context of a project for the propagation of Cyclamen persicum (cyclamen) the proteins of zygotic and somatic embryos of this plant were comparatively examined . The identified proteins are assigned to 30 different metabolic paths in 10 different metabolic areas. Abundance differences of proteins in the two fractions examined can be filtered out and the corresponding proteins visualized on the gel image.
The subject of another project was the analysis of the mitochondrial proteome of the model plant Arabidopsis thaliana . In this project a special 2D PAGE system was used, in which protein complexes were separated in first gel dimension and the protein sub-units of the complex were separated in the second dimension. Individual proteins can be allocated to the protein complexes on the basis of their vertical positions. In the context of this project, more than 35 different protein complexes were able to be identified.
Production of GelMaps
The platform operates as a completely server-based web tool and therefore does not require any software installation or mandatory registration. All that is required is a JPEG file of the gel and a prepared table with protein data (fig. 3). The data table must contain at least the coordinates and the title of the spot in order to assign the data to a spot on the map. However, the user can specify up to 25 further freely named information fields for each spot. The creation of a project takes less than a minute: both files are uploaded to the server, where the project can receive a titel and optional password protection. There they are entered into a database and the user receives the short URL to his or her GelMap project, which can then be passed on, e.g. http://gelmap.de/47. With the aid of an administrator password, the project can be deleted at any time if the upload of a new version is desired. In the meantime, many projects have already been annotated via the GelMap portal. The authors will be glad to answer queries from people who are interested.
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