Rosetta Elucidator System

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract The Rosetta Elucidator Protein Expression Data Analysis system is a comprehensive solution for organizations involved in protein expression analysis. It meets the challenges of proteomics research by providing capabilities to support mass-spectrometry-based, gel-free protein biomarker discovery. The system includes raw data management, liquid chromatography/mass spectrometry (LC/MS) data processing for quantitative and differential analysis, protein identification and high level analysis at the peptide and protein level.

Products key features/capabilities include:

Data Management -- Built on Rosetta Biosoftware’s stable platform for the management of expression data, the Elucidator system is a complete data management solution for end-to-end proteomics data analysis. The system can scale to meet the infrastructure needs from small-scale to the largest proteomics projects. The Elucidator system enables you to:

1) Store and manage large volumes of mass spectrometry data.

2) Spend less time loading and formatting data with the Elucidator system's auto-importing tools.

3) Manage raw data, processed data, and associated protein annotations in one software solution.

Retrieve and view data at multiple summarization levels (e.g., feature (peak), isotope group, charge group, peptide, and protein-level data). Support for Multiple Workflows and Instruments -- The Elucidator system supports multiple workflows for the analysis of proteins, including label-free LC/MS, shotgun (Analyze data in two shotgun modes: quantitative or spectral counting), and Stable Isotope Labeling with Amino acids in Cell culture (SILAC). Each workflow can be used with data from multidimensional separations. The Elucidator allows for integration with an ever expanding list of instruments from several vendors.

Peak Detection -- The PeakTeller algorithm in the Elucidator system provides sensitive peak detection, and accurate peak extraction and quantitation from complex mass spectrometry data. Novel image processing steps of the PeakTeller algorithm generates processed, or aligned, data from label-free LC/MS experiments based on your experimental parameters. To effectively identify differentially expressed peaks (features) and receive accurate quantitation for each peak, the Elucidator system allows you to:

1) Correct for run-to-run retention time variations by accurately aligning data from the differential LC/MS workflow across runs via the PeakTeller algorithm.

2) Use built-in statistical methods to maximize detection of differentially-expressed peaks and minimize false positives - even when few experimental replicates are available.

3) Take advantage of the automated de-isotoping and charge deconvolution of peptides to analyze data at multiple summarization levels.

4) Visualize raw and aligned data using the Peak Viewer.

Peptide and Protein Identification -- Seamless integration with database search engines and open source tools built into the Elucidator system help you to efficiently identify proteins. Create peak list (DTA) files, submit to search engines, and import results for streamlined peptide and protein identification.

1) Integrate with Sequest, MASCOT (see G6G Abstract Number 20087), and X! Tandem search engines.

2) Manage peptide and protein database search results.

3) Verify correct peptide/protein assignments for all features with PeptideProphet and ProteinProphet.

4) View search results, the theoretical spectrum, and other information related to individual features with the Verification Viewer.

Experimental Definition -- Analyze complex experimental designs effectively with the Experiment Definition feature in the Elucidator system. This feature controls the processing of raw data files to create processed data types based on the parameters of your experiment. These are the basis for all subsequent data analyses in the system. The Elucidator system supports data management and analysis for both simple and complex experiments that contain multiple factors and levels. For example, you can design an experiment that contains samples from different doses, various time points, and different treatment groups.

Analysis Tools -- Save time by performing all your work in the Elucidator system: access data and perform statistical analyses for multiple workflows in one proteomics software solution. The Elucidator system provides you with a comprehensive data mining and analysis toolset - for novice and expert users - that includes:

1) Workflow interface for tracking the progress of each task in your end- to-end analysis.

2) Parametric and non-parametric significance tests, such as Analysis of Variance (ANOVA), Wilcoxon, and t-Tests.

3) Data reduction methods [Multidimensional Scaling and Principal Component Analysis (PCA)].

4) Supervised learning methods (classifiers).

5) Hierarchical and partitioning clustering methods, trend analysis.

6) Plots and interactive MS data viewers.

7) Visual scripts for data analysis for automating frequently-used workflows.

8) Ability to incorporate publicly available statistical tools or your own custom algorithms written in the R programming language for statistical computing.

Services and Support -- Rosetta Biosoftware is a dedicated group of technology professionals and scientists committed to providing research organizations and users with information, tools and the support needed to make their research efforts successful.

1) Rosetta Professional Services can help you customize and integrate the Elucidator system with your current protein expression research efforts and existing bioinformatics tools.

2) Rosetta Technical Account Managers (TAMs) are trained scientists for routine or advanced support.

3) Application Scientists experienced in the mass spectrometry, proteomics, and informatics fields provide training which can be custom-tailored for your workflows.

System Requirements

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Manufacturer Web Site Rosetta Elucidator System

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G6G Abstract Number 20086

G6G Manufacturer Number 102303