ProteinChip Data Manager Software



SELDI Citations
SELDI Citations Database

SELDI Citations Database

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Biomarker Discovery Using SELDI Technology

Proper study and experimental design coupled with the correct data analysis approach are critical components of successful biomarker discovery, no matter which technology, platform, or workflow is used. Bio-Rad has produced two in-depth guides to provide researchers with strategies for success.

The first guide, Biomarker Discovery Using SELDI Technology — A Guide to Successful Study and Experimental Design, provides a series of general guidelines for effective study design using virtually any proteomics technology, and gives specific recommendations for using the ProteinChip surface-enhanced laser desorption/ionization (SELDI) system. This guide also includes:

  • Guidelines for proper sample selection, collection, handling, and storage
  • Instructions for planning the experimental workflow
  • Tips on improving reproducibility through standard operating procedures
  • Important considerations for data analysis implementation
  • Optimized methods and protocols for serum or plasma analysis

The second guide, Biomarker Discovery Using SELDI Technology — A Guide to Data Processing and Analysis Using ProteinChip Data Manager Software, is a comprehensive resource for data analysis workflows, guidelines, and specific recommendations for analyzing biomarker discovery data. The guide covers:

  • General data analysis workflows
  • Data organization
  • Data processing steps, including baseline subtraction, normalization, and spectrum alignment
  • Statistical analysis using P values and ROC curves, hierarchical clustering, and principal component analysis
  • Glossary of software terms

Operational Qualification Report

Operational Qualification Reporting

As with any scientific study, the calibration of the platform must be monitored closely at regular intervals to ensure maximum reproducibility. The software works in conjunction with the ProteinChip operational qualification (OQ) kits to provide calibration results for the ProteinChip SELDI reader from a single mouse click. The software automates the application of necessary processing parameters, labels the required peaks, and generates a PDF report of the results.

OQ report.

What's New in Version 4

New Features in ProteinChip Data Manager Software, Version 4
ProteinChip data manager software, version 4 is the latest version release for the ProteinChip SELDI system, Bio-Rad's high-sensitivity, high-throughput biomarker discovery platform. Version 4 introduces several new features that enhance the biomarker analysis workflow, including a number of new data visualizations and improvements to spectral navigation.

  • Data processing, normalization, and clustering have been brought together into a new Analysis Wizard; parameters set in the Analysis Wizard can be saved and rapidly applied to other data sets
  • Overlay plots are now available for visualizing protein expression differences between spectra
  • Spectrum traces can now be assigned colors for easy identification in an overlay plot
  • Trend plots allow plotting of clustered data along an additional time point axis in order to visualize the expression level of a cluster as a function of time or dosage
  • Navigation of spectra has been modified to provide better flexibility and speed when browsing spectra

New overlay plot with spectrum coloring.

New trend plot.

Software Configurations
  Enterprise Edition Personal Edition Desktop Edition
Protein profiling data analysis toolset Yes Yes Yes
SELDI reader control Yes Yes No
OQ kit compatibility Yes Yes Yes
Sample tracking with Virtual Notebook Yes No No
Audit trail Yes No No
Server/client Yes Yes No
Offline data analysis No No Yes

Successful biomarker discovery projects require screening large volumes of data to distinguish clinically relevant information from normal biologic diversity. More than simply data acquisition software, ProteinChip data manager software tracks samples and manages the complex data inherent to biomarker discovery. Software analysis features provide powerful, advanced data mining and analysis capabilities for rapid, automated analysis of multiple experiments over many conditions to identify potential biomarkers. The server editions (Personal and Enterprise Editions) of the software are included as part of the respective ProteinChip SELDI systems.

The stand-alone ProteinChip data manager software, Desktop Edition provides users with all the analysis features of the server versions, and allows them to perform data analysis while separated from the instrument computer. Customers can upgrade their existing version 3.x servers by purchasing the upgrade 3.x to 4 package.

Informatics Support for the Protein Profiling Workflow

ProteinChip data manager software improves the efficiency of the ProteinChip SELDI system workflow, providing scalability from small data sets to very large experiments and enabling processing and analysis of thousands of spectra. Built-in query tools allow rapid searching of the centralized database, and the intuitive graphical user interface and folder structure facilitate data management.

Automated Sample Tracking

The Virtual Notebook feature provides an intuitive graphical user interface for fast, easy input of sample information. This electronic laboratory notebook provides the ability to enter information about sample processing conditions and to apply these properties virtually to spots on the arrays. This can be done before running arrays through wet-lab processes and can serve as a map to guide laboratory work, saving hours of manual postacquisition annotation.

Integrated Data Mining and Analysis

The software's data mining capabilities enable rapid analysis and comparison of thousands of spectra across many conditions in a single run. Analysis features include proprietary algorithms for the identification of significant changes in protein expression levels and possible biomarkers. Statistical information is then displayed in a multitude of graphical visualizations and tables. Powerful statistical tools include principal component analysis (PCA), receiver operating characteristic (ROC) plots, and hierarchical clustering with a heat map view.

Security and Traceability

ProteinChip data manager software's security implementation allows multiple groups of users to use a centralized database while working independently. The built-in audit trail feature maintains a record of changes made to the data.

ProteinChip Data Manager Software 4, Enterprise Edition

5-user network license, control and analysis software for the ProteinChip SELDI system, Enterprise Edition

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(Discontinued) ProteinChip Data Manager Software 4, Personal Edition

1-user network license, control and analysis software for the ProteinChip SELDI system, Personal Edition

This product is no longer available. Please contact technical support for more information on replacement product.
ProteinChip Data Manager Software 4, Desktop Edition

1-user network license, analysis software for the ProteinChip SELDI system, Desktop Edition

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ProteinChip Data Manager Software 4, Add 1 User to Network License

Adds 1 user to existing network license for ProteinChip data manager software

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ProteinChip Data Manager Software 4 Upgrade

Version 3.x to 4 upgrade for ProteinChip data manager software

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ProteinChip Data Manager Software, Desktop Edition and Server Upgrade Bundle

1-user network license, analysis software for the ProteinChip SELDI system, Desktop Edition; includes version 3.x to 4 upgrade

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Number Description Options
5530 ProteinChip SELDI System Brochure, Rev A Click to download
5526 ProteinChip Data Manager Software Flier, Rev B Click to download
10008220 Instruction Manual, ProteinChip SELDI System: Personal Edition and Enterprise Edition, Rev C Click to download