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Information System for Proteome Studies

You spend a lot of time and resources on generating your proteomics data – maximize the information you get out of it!

Protecs is an information system that supports teams of life science researchers in conducting proteomics studies. With Protecs you can organize all relevant data in one central location and make it available on the intranet or publish it on the internet. With its integration of gel preparation, image analysis, and protein identification, its flexible cross linking, near-zero maintenance and fine-grained access control, Protecs is the choice for teams wanting to streamline their workflows and extract the maximum of results from their experiments.

Easily adaptable to your application

For every application, the administrator can define a set of application specific parameters such as tumor stage, tumor size etc. for tumor studies, or bacterial strain, medium and cultivation conditions for studies of bacterial physiology. This makes Protecs adaptable to a wide range of application scenarios, from bacterial stress response to the molecular anatomy of tumors. Application specific parameters are defined by the customer and can be changed any time.

Enabling collaboration

A fine-grained system of access rights makes sure that only authorized users can see or modify a certain piece of data. For example, you can show finished work to clients or publish it on the intranet, while keeping work in progress private. You can even publish selected results on the web. As a principle, Protecs stores any piece of data together with information about its generation, so you can track by whom and when that spot was identified or that gel was made. Gels, images, mass spectra etc. are grouped into experiments which can in turn be grouped to form projects. That way you can separate data for different projects or customers.

Streamlining the proteomics workflow

With Protecs as a central repository, teams get a continuous flow of information from experimental setup to gel image analysis and protein identification. Using Protecs will decrease substantially the amount of coordination necessary and support well-standardized and well-documented procedures.

2D gel image analysis

Protecs can be closely integrated with Delta2D, the leading 2D image analysis software developed by DECODON. This combination yields a seamless workflow from gel production to image analysis to protein identification. Delta2D can be used to do a wide range of quantitative analysis and visualization on protein expression profiles, as well as for controlling spot picking devices.

Protein identification

Protecs can store one or more identified proteins for a spot, including post-translational modifications. Protein identifications can be displayed as annotations on a gel image inside a web browser. Mass spectra, peak lists and hit lists can be stored, allowing you to trace protein identifications back to the raw data. Protecs has a direct connection to web-based MS fingerprint analysis software that automates the spectrum – peak list – hit list process. For each MS analysis, Protecs stores the software version and database version that was used, so you can redo the analysis later should new software or data bases become available.

Accessing Genome and Proteome Data

Basic data about genomes and proteomes is stored in Protecs to make it available under a uniform data model. One Protecs installation can contain data for multiple organisms. Additional external accession numbers (such as Genbank accession numbers) can easily be attached to genes and proteins. Protecs can translate between different accession number systems, and even between multiple versions of an external database. For example, you can display today's protein names for a gel that was annotated two years ago.

Protecs as part of the informatics infrastructure

Protecs was designed to be easily embedded into existing bioinformatics infrastructure.

Near zero maintenance

Protecs and its underlying Caché database technology require very little maintenance, making it ideal for teams with little or no IT support resources.

A choice of connections

Protecs can be connected to in-house databases or LIMS by a variety of technology standards, such as XML, web services (SOAP), CORBA, or ODBC.

Systems architecture