Chromatographic Surfaces

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Bar Code Lookup Table

Bar code lookup table on the ProteinChip SELDI reader.

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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

ProteinChip Array Selection Guide
General Description Array Surface Chemistry (active spots) Applications
Strong Anion Exchange
Capture of molecules that have negative surface charges Q10 Cationic, quaternary ammonium groups that interact with the negative charges on the surface of target proteins; for example, aspartic or glutamic acid
  • Selective analysis of proteins with low pls
  • Biomarker discovery
Weak Cation Exchange
Capture of molecules that have positive surface charges CM10 Weak anionic carboxylate groups that interact with the positive charges on the surface of the analyte; for example, lysine, arginine, or histidine
  • Selective analysis of proteins with high pls
  • Biomarker discovery
IMAC
Capture of molecules that bind polyvalent metal ions, such as nickel, copper, zinc, iron, and gallium IMAC30 NTA groups that chelate metal ions. Proteins applied to the array surface may bind to the chelated metal ion through histidine, tryptophan, cysteine, and phosphorylated amino acid residues
  • Analysis of metal-binding, phosphorylated, or polyhistidine (His)-tagged proteins
  • Biomarker discovery
Hydrophobic/Reverse-Phase
Capture of large proteins through hydrophobic or reverse-phase interactions H50 Methylene chains that closely mimic the characteristics of C6 to C12 alkyl chromatography media
  • Protein profiling
  • Purity determination
  • Rapid protein analysis
  • Calibration with proteins of known MW
  • Biomarker discovery
Capture of smaller proteins and peptides through hydrophobic and reverse-phase interactions H4* Active spots contain chains of 16 methylene groups that bind proteins through reverse-phase chemistry. Binds proteins abundant in alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, or tyrosine
  • Purity determination
  • Rapid protein/peptide analysis
  • Biomarker discovery
Analysis of peptides resulting from tryptic digestion of proteins SEND ID Chains of 18 methylene groups (C18) that bind peptides through reverse-phase chemistry; matrix is integrated into the array surface
  • Peptide mass fingerprinting
Normal Phase
General protein binding surface; recommended for hydrophilic proteins NP20 Silicon dioxide, which allows proteins to bind via serine, threonine, or lysine residues
  • Quick protein analysis
  • Purity determination
  • Verification of the presence or absence of a molecule
  • Calibration with peptides or proteins of known MW
Preactivated Surface
Covalent immobilization of biomolecules for subsequent specific capture of proteins from complex samples PS10 Reactive acyl imidazole moieties
  • Analysis of antibody-antigen, receptor-ligand, protein-protein interactions
  PS20 Epoxy groups  
  RS100 Reactive acyl imidazole moieties on a hydrogel backbone  
Nonreactive Surface
  Au Gold provides a nonreactive surface for general protein analysis (limited reusability)
  • Quick protein analysis
  • Calibration with peptides or proteins of known MW

*Array lacks the hydrophobic coating needed for sample containment; a hydrophobic PAP pen can be used to manually create the barrier.

SELDI Citations
SELDI Citations Database
 

SELDI Citations Database

ProteinChip chromatographic surface arrays provide a relatively high capacity and bind a large variety of proteins and peptides for a wide range of protein profiling applications. Each array mimics a traditional chromatographic surface, such as cation/anion exchange, metal affinity, or hydrophobic/hydrophilic. Arrays feature eight 2 mm diameter spots (A–H format) that correlate with the spacing of wells in a single column on a standard 96-well microplate (9 mm well pitch). A unique bar code and serial number are printed on the back of each array for traceability.

Refer to the ProteinChip Array Selection Guide for more information on selecting arrays with the appropriate surface chemistries

ProteinChip Gold Array

C55-30033
Pkg of 1, A–H format, gold array for use with the ProteinChip SELDI system

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ProteinChip H4 Arrays

C57-30028
Pkg of 12, A–H format, reverse-phase arrays for use with the ProteinChip SELDI system

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ProteinChip H50 Arrays

C57-30065
Pkg of 12, A–H format, hydrophobic/reverse-phase arrays for use with the ProteinChip SELDI system

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ProteinChip IMAC30 Arrays

C57-30078
Pkg of 12, A–H format, immobilized metal affinity chromatography arrays for use with the ProteinChip SELDI system

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ProteinChip NP20 Arrays

C57-30043
Pkg of 12, A–H format, silicon dioxide arrays for use with the ProteinChip SELDI system

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ProteinChip Q10 Arrays

C57-30080
Pkg of 12, A–H format, strong anion exchange arrays for use with the ProteinChip SELDI system

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Number Description Options
5530 ProteinChip SELDI System Brochure, Rev A Click to download
5524 ProteinChip Arrays and Reagents Product Information Sheet, Rev C Click to download
5908 Top-Down, Bottom-Up: The Merging of Two High-Performance Technologies, Rev A Click to download
10008230 Instruction Manual, ProteinChip H50 Array (Reverse Phase), Rev G Click to download
10008237 Instruction Manual, ProteinChip Q10 Array (Strong Anion Exchanger), Rev F Click to download
10008236 Instruction Manual, ProteinChip IMAC30 Array (Immobilized Metal Affinity Capture), Rev F Click to download
10008235 Instruction Manual, ProteinChip CM10 Array (Weak Cation Exchanger), Rev G Click to download
10008243 Instruction Manual, ProteinChip Gold Array, Rev F Click to download
10008233 Instruction Manual, ProteinChip NP20 Array (Normal Phase), Rev H Click to download
10008422 Instruction Manual, ProteinChip 8-Well Bioprocessor User Guidelines, Rev B Click to download
10008232 Instruction Manual, ProteinChip H4 Array (Reverse Phase), Rev F Click to download