ProteinChip Pattern Analysis Software



SELDI Citations
SELDI Citations Database

SELDI Citations Database

Request a Biomarker Discovery Guide

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

ProteinChip pattern analysis software allows simultaneous analysis of multiple biomarkers. Tracking multiple biomarkers increases statistical power, providing superior predictive value and greater utility in diagnosis, toxicology, patient stratification, and patient monitoring. The ability to detect patterns formed by multiple biomarkers greatly improves the sensitivity and specificity of an assay. With ProteinChip pattern analysis software, you can collect reproducible protein expression data on hundreds of proteins at once — opening the door to rapid, simplified pattern analysis.

Discover Predictive Protein Biomarker Patterns
Subtle variations found in SELDI data from clinical samples indicate that certain patterns of protein expression can predict phenotypes, such as the presence or absence of a certain disease, a particular stage of cancer progression, or a positive or adverse response to drug treatment. ProteinChip pattern analysis software supports both the discovery of multiple protein biomarkers and their translation to assays with high predictive accuracy. A particularly valuable feature of this software is that it provides a hierarchy of presumptive protein biomarkers that users can then proceed to identify, expediting the discovery of relevant functional information about the proteins.

Classify Samples Using the Decision Tree Model
Starting with SELDI peak intensity values from a "training set" of samples, ProteinChip pattern analysis software defines a single splitting rule that best segregates the training set by phenotype. The software repeats this process on each resulting subclassification of the data to produce a decision tree that describes the best set of rules for organizing the samples according to phenotype.

Incorporate Clinical Sample Information
Classification algorithms allow incorporation of non-SELDI data into the analysis. This can result in a better overall decision tree and help elucidate complex relationships between protein expression profiles and clinical data.


ProteinChip Pattern Analysis Software 5.0

5-user network license for ProteinChip pattern analysis software

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(Discontinued) ProteinChip Pattern Analysis Software 5.0 Upgrade

Software version 4.0 to 5.0 upgrade, for ProteinChip pattern analysis

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ProteinChip Pattern Analysis Software 5.0, Add 1 User to Network License

Adds 1 user to existing network license for ProteinChip pattern analysis software

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