Overview

 

RADARS/MS: high volume proteomic intelligence platform

Our flagship product, Radars/MS™ (Rapid Data Archival and Retrieval System), is an enterprise class, integrated scientific intelligence platform for the proteomic laboratory. The solution incorporates several client/server, database and extranet applications offering discovery, analysis and delivery applications. It offers the fastest, most reliable and most seamless solution for protein identification currently available.

fig 1 RADARS/MS architecture

The need for a solution like radars/ms

Proteome analysis is becoming a method of choice for the elucidation of protein function and is being applied as a tool in the drug discovery process and for locating disease markers. In a typical proteome project the protein content of two collections of cells are compared. The comparison can be between wild-type and mutant cells or between cells that have been exposed to different environments. Differential display of the protein content can be obtained by lysing and fractionating the cells, followed by protein separation with gel electrophoresis. Spots on the gels that differ between the two collections of cells are cut out, digested with a protease, and analyzed with mass spectrometry. Proteome projects are inherently large scale and therefore generate massive amounts of experimental data.

 

RADARS/MS features and benefits

RADARS/MS was designed as a distributed system to be flexible and scalable. The flow of experimental data into the system is depicted in Figure 1. A web browser is used to set up the framework of the organization of the experimental data: experimental details can be specified and the type of data processing desired. RADARS/MS provides the high level of automation and seamless integration between data analysis and data storage that is required for rapid discovery and validation of new drug targets and disease markers.

·         Storage of experimental data and analysis results from high-throughput proteome projects in a relational database.

·         Fully automatic analysis of large collections of mass spectra.

·         Fast, automated sequence database searches for protein identification using information from MS peptide maps and MS/MS spectra.

·         Rapid characterization of post-translational modifications of proteins.

·         Clear and efficient visualization of data and analysis results.

 

RADARS/MS Database Model

The data in RADARS is organized in projects and experiments. Each mass spectrum can be analyzed (peaks assigned) in different ways by applying different analysis methods (defining parameters for how the spectrum is processed, e.g. filters and signal-to-noise ratio threshold). The peak list resulting from each analysis is stored in the database and can be used in a database search for protein identification by applying a comparison method (defining the chemistry, e.g. enzyme and modifications) and a database search method (defining the database search parameters, e.g. taxonomy and protein mass).

fig 2 RADARS Database Model

 

RADARS/MS Administrator

The RADARS Administrator handles all the communication with the user, the relational database and the application servers. The user can point a browser to the RADARS Administrator to be able to:

·         Define methods for spectrum analysis and database searches (Figure 3).

·         Schedule analyses and searches.

·         Administer the RADARS Demon running on the application servers.

·         Synchronize the file server and the database (Figure 4).

·         View reports of results (Figure 7-8).

 

The RADARS Demon contacts the RADARS Administrator to (Figure 5-6).

·         Obtain a list of scheduled tasks.

·         Save results of analyses and database searches.

 

Figure 3 The flow of information when the user interacts with RADARS

 

 

Figure 4. Generating mass spectra

 

Figure 5. Automated mass spectrum analysis

 

Figure 6. Automated datamining for protein identification

Figure 7. Knowledge delivery

 

Radars administrator interface

 

Figure 8. Knowledge delivery: the RADARS user interface showing a report on the search results for the mass spectra in an experiment. 


RADARS/MS Application Server

 

The RADARS Demon is handling the communication between the RADARS Administrator and the applications running on the application server, i.e. requesting new task and saving results (Figure 8).

 

Applications

 

fig 9 server applications managed by the RADARS DEMON

The scientific intelligence within RADARS/MS resides between the BIOML powered administrator and databases and our suite of server applications, managed by the RADARS DEMON. One of the benefits of the relationship between the administrator and the DEMONS is that we are able to chain multiple servers and multiple clients together to leverage the massive volume of data archived in our databases.

Throughput of analytic results from clustering ENTERPRISE M/Z servers, for example can exceed 5,000 peak extractions per hour, sustained. Processes utilizing our rapid retrieval routines run even fatser. These procedures are automated, freeing up technicians and scientists to interpret results and apply knowledge learned or generate more data from experiments, while the DEMON runs.

 

RADARS/MS Client Applications

 

The RADARS Client Applications are Windows applications that can be used for detailed investigation of the results:

CLIENT M/Z - a program for viewing and manipulating biopolymer mass spectra that is capable of performing a wide variety of tasks, some manual and some automated, such as peak labeling, calibration, and automatic data entry into ProFound and Sonar MS/MS. M/Z is used with RADARS/MS to view details of the results of automatic peak labeling and peptide assignment.

 

Figure 10. The M/Z user interface.

 

PMX/ PAWS - the Protein Analysis Work Sheet allows visualization of a peptide or protein and its cleavage fragments. A virtual experiment may be performed on the sequence or modified sequence. PAWS searches for peptides of user-defined mass sizes. The residues are highlighted on the primary sequence display, and PAWS maps the fragments along a representation of the full-length sequence (coverage maps).  

Figure 11. The PAWS user interface.


BIOBROWSER

BioBrowser is an application for viewing and effectively communicating information about proteins and nucleic acids.

 

It is based on BioML - an XML language for that captures the information present in a molecular biology database and provides a true representation of the underlying biology.

 

Figure 12. The BioBrowser user interface.