Mass Spectrometry in Protein Biomarker Applications: Software, Services, and Instrument Markets

Table of Contents

Chapter One: Executive Summary

• Proteomics Tools, Approaches in Drug Discovery, Biomarker Discovery
• Biomarker Validation, Diagnostics, Prognostics
• Sources of Samples
• Biomarkers in Pharmaceutical Industry, Diagnostics Industry
• Drug Discovery and Development
• Diagnostics
• Scope and Outline
• Market Summary

Chapter Two: Introduction

• Historical Background
  • Definitions
  • Biomarkers
  • Screening Markers
  • Prognostic Markers
  • Staging Markers
  • Stratification Markers
  • Efficacy Markers
  • Target Markers
  • Toxicity Markers
  • Antecedent Markers
  • Translation Markers
  • Surrogate Markers
  • Positive Predictive Value (PPV)
  • Sensitivity
  • Specificity
• Value of Biomarkers in Industry
• Mass Spectrometry in Proteomics
  • Software
  • Tandem Mass Spectrometry
  • Types of Mass Spectrometers Used for Protein Biomarkers
  • MALDI-TOF
  • TOF / TOF
  • Triple Quad
  • Quadrupole TOF
  • Quadrupole Ion Trap
  • Fourier Transform MS (FTMS / FT-ICR-MS)
• Biomarker Discovery
  • MS in Biomarker Applications
  • Biomarker Discovery Process in Diagnostics
  • Biomarker Discovery in Drug Development
• Biomarker Validation
  • Validation Process in Drug Discovery and Development
  • Validation Process in Diagnostics

Chapter Three: Disease Application Areas

• Cancer
  • Prostate
  • Prostate Cancer Related Articles:
  • Breast
  • Breast Cancer Related Articles:
  • Lung
  • Ovarian / Endometrial
  • Ovarian Cancer Related Articles:
  • Oral / Lymphoma
  • Oral Cancer Related Articles:
  • Liver
  • Other / Multiple Cancers
  • General Cancer Related Articles:
• Cardiovascular Disease
• Neurological Disease
  • Parkinson' s Disease
  • Alcohol Abuse
  • Sleep Apnea
  • Cerebral Injury
  • Amyotrophic Lateral Sclerosis (ALS)
• Diabetes
• Aging
  • Aging Related Articles:
• Sepsis

Chapter Four: Proteomics Tools

• Introduction
• 2D Gel Electrophoresis (2DGE)
• Recent Developments in 2DGE
• Liquid Chromatography (LC)
• Recent Developments in LC
• Protein Chips

Chapter Five: Trends

• Industry Trends
  • MS Vendors Creating Biomarker Divisions, Collaborations
  • Some Acquisition, Consolidation Trends in Recent Years
  • Regulatory Environment Becoming More Clearly Defined
  • Drug Companies' Woes Bringing Growth in Biomarkers
  • Intellectual Property Defines Companies' and Instruments' Territories
  • Diagnostics Industry Facing Uncertain IP Issues
  • Globalization and Diversity Converging Rapidly
  • Technology Trends
    • Ongoing Debate, Confusion Over Protein Patterns Vs Identified Markers
    • Emphasis on Sample Preparation, Fractionation
    • High Abundance, Low Abundance, Both
    • LC and ESI Approaches Growing Relative To 2DGE and MALDI
    • New Combinations of LC, ESI, and MALDI
    • Integration and Automation
    • Advances in Labels to Address Focused Applications
    • Biomarkers for Classes of Drugs
    • Chemogenomics / Chemoproteomics Techniques Further Driving Advances
    • Direct Analysis of Tissue
    • Shift to Solid-State Lasers
    • Field Applications Driving Miniaturization

Chapter Six: MS Software Market

• Products and Competitors
  • Agilent Technologies
  • GeneSpring MS
  • MassHunter
  • SpectrumMill
  • Applied Biosystems / MDS Sciex
  • Analyst
  • MarkerView
  • Pro QUANT
  • ProteinPilot
  • Bruker Biosciences
  • ClinProTools
  • flexImaging
  • Cerno Biosciences
  • MassWorks
  • Correlogic Systems
  • Proteome Quest
  • GeneData AG
  • Expressionist Pro
  • GenoLogics Life Sciences Software
  • Proteus
  • Insightful Corp
  • S+Proteome
  • Genstruct
  • Molecular Epistemics platform
  • Matrix Science
  • Mascot
  • Nonlinear Dynamics
  • Progenesis PG600
  • Thermo
  • SIEVE
  • Public Domain Tools and Databases
• Revenue and Growth Forecast

Chapter Seven: MS Services Market

• Competitors
  • BG Medicine
  • Biophysical Corporation
  • Caprion Pharmaceuticals
  • Celera Diagnostics
  • Compugen
  • Panatecs
  • Power3 Medical Products
  • Predictive Diagnostics
  • Protein Discovery, Inc
  • RxGen PrimaTox
  • SurroMed
• Revenue and Growth Forecast

Chapter Eight: MS Instrumentation Market

• Products
  • Agilent Technologies (Palo Alto, CA)
  • Agilent 1200 Series HPLC-Chip/MS System
  • Agilent 3100 OFFGEL Fractionator
  • Agilent 6210 TOF
  • Agilent 6340 Ion Trap Liquid Chromatograph/Mass Spectrometer (LC/MS)
  • Agilent 6510 Q-TOF LC/MS
  • Multiple Affinity Removal System 7 LC Column and Spin Tube
  • Applied Biosystems / MDS Sciex (Foster City, CA ; Ontario, Canada)
  • 3200 Q TRAP LC/MS/MS System for Proteomics Applications
  • 4000 Q TRAP LC/MS/MS System for Proteomics Applications
  • 4800 MALDI-TOF/TOF
  • ICAT Reagents
  • iTRAQ Reagents
  • QSTAR Elite LC/MS/MS
  • MIDAS TRAQ Systems
  • Becton Dickinson (Franklin Lakes, NJ)
  • P100 Sample Collection Tubes
  • Beckman Coulter (Fullerton, CA)
  • ProteomeLab IgY-12 Partitioning Chemistries
  • Bruker Biosciences (Billerica, MA)
  • apex-Qe
  • autoflex II, autoflex II TOF/TOF
  • ClinProt Large-Protein Beads
  • ClinProt Micro
  • ClinProtRobot
  • Isotope Coded Protein Labels (ICPL) Triplex Kit
  • MALDI Molecular Imager
  • microflex, microflex LT
  • Protein Post-Translational Modification (PTM) Discovery Tool
  • ultraflex, ultraflex TOF/TOF
  • Expression Pathology (Gaithersburg, MD)
  • Liquid Tissue MS Protein Prep Kit
  • PerkinElmer (Wellesley, MA)
  • prOTOF 2000 MALDI O-TOF
  • Qiagen (Venlo, The Netherlands)
  • MSXpress Protein Chip
  • Shimadzu / Kratos (Kyoto, Japan)
  • LCMS-IT-TOF
  • Thermo Electron (Waltham, MA)
  • LTQ XL
  • LTQ FT
  • LTQ Orbitrap
  • MDLC LTQ LC-MS
  • Waters (Milford, MA)
  • LCT Premier XE
  • micro MX
  • Protein Expression System
  • Q-Tof Premier
• Total Market Size and Growth Forecast
• The Market by Disease Area
• Competitive Analysis: Market Share by Vendor
• Market Share by Product Type

Chapter Nine: Consortia and Alliances

• The Biomarker Alliance
• Biomarkers Research Initiatives in Mass Spectrometry (BRIMS)
• Clinical Proteomic Technologies Initiative for Cancer
• Clinical Plasma Profiling Consortium
• Early Detection Research Network (EDRN)
• HUPO Plasma Proteome Project
• Oncology Biomarker Qualification Initiative (OBQI)
• Pharmacogenomics Research Network (PGRN)
• Predictive Safety Testing Consortium

Chapter Ten: Company Profiles

• Agilent Technologies (Palo Alto, CA)
• Applied Biosystems / MDS Sciex (Foster City, CA ; Ontario, Canada)
• Bruker BioSciences (Billerica, MA)
• Ciphergen Biosystems (Fremont, CA) (Bio-Rad)
• GE Healthcare Bio-Sciences (Little Chalfont, United Kingdom) -
• formerly Amersham Biosciences (Uppsala, Sweden)
• PerkinElmer (Wellesley, MA)
• Thermo Electron (Waltham, MA)
• Waters (Milford, MA)

Chapter Eleven: Deals

Chapter Twelve: Academic / Government / Non-Profit Research

• The Center for Biomarker Research
• Johns Hopkins Center for Biomarker Discovery
• Plasma Proteome Institute

Chapter Thirteen: Competitive or Disruptive Technologies

• Protein Arrays, Chips
  • Invitrogen ProtoArray
  • Protneteomix Protein, Peptide and Antibody Arrays
  • Whatman Schleicher & Schuell Serum Biomarker Chip
  • Array of Micromachined Ultra Sonic Electrospray (AMUSE)
  • Monogram Biosciences' (formerly Aclara) eTag Technology
  • Imaging-Based Techniques
  • ELISA

Chapter Fourteen: Challenges

• Debate Over Serum Proteomics and Biomarkers
• Advances in Competing, Complementary Techniques, Software Erode Sales
• Reproducibility is Key Priority But Elusive
• Clinical Research Not Yet Experienced With Biomarkers, Procedures
• Blockbuster Mentality Creates Obstacles for Biomarkers
• Gap Between Pharmaceuticals and Diagnostics Still Wide
• Large Investment Required for Biomarker Validation Creates Gap
• Dropping Prices Hurt Revenues, Confuse Customers
• Regulatory and Ethical Issues Not Completely Resolved
• Feasibility of Biomarker Approaches Still Unproven
• Data Analysis Bottleneck Slows Momentum

Chapter Fifteen: Strategic Recommendations

• Recommendation 1: Software
• Recommendation 2: Consumables
• Recommendation 3: Standards, Quality, and Data Exchange
• Recommendation 4: Reliability and User-Friendliness
• Recommendation 5: Systems Biology
• Recommendation 6: Partnering for Novel Technologies
• Recommendation 7: Drug and Diagnostics Partnerships
• Recommendation 8: Training and Education

List of Exhibits

Chapter One: Executive Summary

• Figure 1-1: Market Summary: MS for Protein Biomarker Applications 2005-2011

Chapter Six: MS Software Market

• Table 6-1: The World Market for Protein Biomarker MS Software (Revenues) 2005-2011
• Figure 6-1: Trending in the Revenues for Protein Biomarker MS Software 2005-2011
• Table 6-2: The World Market for Protein Biomarker MS Software (Growth) 2005-2011
• Figure 6-2: Trending in the Growth of Protein Biomarker MS Software 2005-2011

Chapter Seven: MS Services Market

• Table 7-1: The World Market for Protein Biomarker Services (Revenues) 2005-2011
• Figure 7-1: Trending in the Revenues for Protein Biomarker Services 2005-2011
• Table 7-2: The World Market for Protein Biomarker Services (Growth) 2006-2011
• Figure 7-2: Trending in the Growth of Protein Biomarker Services 2006-2011

Chapter Eight: MS Instrumentation Market

• Table 8-1: The World Market for MS Instruments for Protein Biomarker Applications (Revenues) 2005-2011
• Figure 8-1: Trending in the Revenues for MS Instruments for Protein Biomarker Applications 2005-2011
• Table 8-2: The World Market for MS Instruments for Protein Biomarker Applications (Growth) 2006-2011
• Figure 8-2: Trending in the Growth of MS Instruments for Protein Biomarker Applications 2006-2011
• Table 8-3: Protein Biomarker MS Revenues and Market Share by Disease Area 2005
• Figure 8-3: Protein Biomarker MS Market Share by Disease Area 2005
• Table 8-4: Protein Biomarker MS Revenues and Market Share by Leading Supplier 2005
• Figure 8-4: Protein Biomarker MS Market Share by Leading Supplier 2005
• Table 8-5: Protein Biomarker MS Revenues and Market Share by Product Type (Ion Trap, MALDI-TOF, Triple Quad, QqTOF, FTMS, Other, Service/Support) 2005
• Figure 8-5: Protein Biomarker MS Market Share by Product Type 2005

Chapter Nine: Consortia and Alliances

• Table 9-1: Early Detection Research Network (EDRN) Awardees (Institution, Organ Focus, Technology/Approach, Industry Collaboration)

Chapter Eleven: Deals

• Table 11-1: Recent Deals, Collaborations, and Alliances