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

Protein biomarkers have become the hot application area for mass spectrometry (MS) and other proteomics-related technologies in the last few years. In the short term, this move towards biomarkers and clinical proteomics research has happened mainly in the drug discovery and development process. However, they also have broad abilities to generate richer information about a disease state, drug response, and/ or the relation between the two; which can be used for diagnostic, prognostic, or various other purposes in the pharmaceutical, diagnostics, and defense industries.

MS has the necessary abilities to rapidly identify biochemicals such as DNA, proteins, or carbohydrates, and thus is currently being used as the workhorse for discovering and validating biomarkers in clinical research, whether for drug development, diagnostic, or other applications. MS technology also far outperforms any alternative for this purpose, due to its particular ability to identify large numbers of components in complex mixtures. These increased abilities have drawn large numbers of life science researchers to procure MS instruments or use available core lab facilities for proteomics experiments.

This report focuses on MS technologies as they are applied to protein biomarker research. It provides in-depth analysis of the markets for:

  • MS Instrumentation,
  • MS Software, and
  • MS Services

In addition to a thorough review of MS products and competitors and the technological and business trends shaping the marketplace, the report provides market data and forecasts for the following as they relate to protein biomarker research:

  • Revenues and growth through 2011 of MS instrumentation
  • Competitive market share by leading supplier
  • Market share by type of MS (Ion Trap, MALDI-TOF, Triple Quad, etc.)
  • Estimated market share by therapeutic area of research
  • Revenues and growth through 2011 for MS services
  • Revenues and growth through 2011 for MS software

The report profiles the top suppliers of MS instrumentation, reviews the regulatory environment, surveys competitive and disruptive technologies, and the details the extensive research collaborations and deals currently underway.


  • 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, OUTLINE, AND METHODOLOGY
    • MARKET SUMMARY
  • Introduction
    • HISTORICAL BACKGROUND
    • DEFINITIONS
    • VALUE OF BIOMARKERS IN INDUSTRY
    • MASS SPECTROMETRY IN PROTEOMICS
      • Software
      • Tandem Mass Spectrometry
      • Types of Mass Spectrometers Used for Protein Biomarkers
    • 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
  • Disease Application Areas
    • CANCER
      • Prostate
      • Breast
      • Lung
      • Ovarian / Endometrial
      • Oral / Lymphoma
      • Liver
      • Other / Multiple Cancers
    • CARDIOVASCULAR DISEASE
    • NEUROLOGICAL DISEASE
      • Parkinson's Disease
      • Alcohol Abuse
      • Sleep Apnea
      • Cerebral Injury
      • Amyotrophic Lateral Sclerosis (ALS)
    • DIABETES
    • AGING
    • SEPSIS
  • Proteomics Tools
    • INTRODUCTION
    • 2D GEL ELECTROPHORESIS (2DGE)
    • RECENT DEVELOPMENTS IN 2DGE
    • LIQUID CHROMATOGRAPHY (LC)
    • RECENT DEVELOPMENTS IN LC
    • PROTEIN CHIPS
  • 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
  • MS Software Market
    • PRODUCTS AND COMPETITORS
      • Agilent Technologies
      • Applied Biosystems / MDS Sciex
      • Bruker Biosciences
      • Cerno Biosciences
      • Correlogic Systems
      • GeneData AG
      • GenoLogics Life Sciences Software
      • Insightful Corp
      • Genstruct
      • Matrix Science
      • Nonlinear Dynamics
      • Thermo
    • Public Domain Tools and Databases
    • REVENUE AND GROWTH FORECAST
      • Table The World Market for Protein Biomarker MS Software (Revenues) 2005-2011
      • Table The World Market for Protein Biomarker MS Software (Growth) 2005-2011
  • 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
      • Table The World Market for Protein Biomarker Services (Revenues) 2005-2011
      • Table The World Market for Protein Biomarker Services (Growth) 2006-2011
  • MS Instrumentation Market
    • PRODUCTS
      • Agilent Technologies (Palo Alto, CA)
      • Applied Biosystems / MDS Sciex (Foster City, CA ; Ontario, Canada)
      • Becton Dickinson (Franklin Lakes, NJ)
      • Beckman Coulter (Fullerton, CA)
      • Bruker Biosciences (Billerica, MA)
      • Expression Pathology (Gaithersburg, MD)
      • PerkinElmer (Wellesley, MA)
      • Qiagen (Venlo, The Netherlands)
      • Shimadzu / Kratos (Kyoto, Japan)
      • Thermo Electron (Waltham, MA)
      • Waters (Milford, MA)
    • TOTAL MARKET SIZE AND GROWTH FORECAST
      • Table The World Market for MS Instruments for Protein Biomarker Applications (Revenues) 2005-2011
      • Table The World Market for MS Instruments for Protein Biomarker Applications (Growth) 2006-2011
    • THE MARKET BY DISEASE AREA
      • Table Protein Biomarker MS Revenues and Market Share by Disease Area 2005
    • COMPETITIVE ANALYSIS: MARKET SHARE BY VENDOR
      • Table Protein Biomarker MS Revenues and Market Share by Leading Supplier 2005
    • MARKET SHARE BY PRODUCT TYPE
      • Table Protein Biomarker MS Revenues and Market Share by Product Type (Ion Trap, MALDI-TOF, Triple Quad, QqTOF, FTMS, Other, Service/Support) 2005
  • 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)
      • Table Early Detection Research Network (EDRN) Awardees (Institution, Organ Focus, Technology/Approach, Industry Collaboration)
    • HUPO PLASMA PROTEOME PROJECT
    • ONCOLOGY BIOMARKER QUALIFICATION INITIATIVE (OBQI)
    • PHARMACOGENOMICS RESEARCH NETWORK (PGRN)
    • PREDICTIVE SAFETY TESTING CONSORTIUM
  • 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)
  • Deals
    • Table Recent Deals, Collaborations, and Alliances
  • Academic / Government / NonProfit Research
    • THE CENTER FOR BIOMARKER RESEARCH
    • JOHNS HOPKINS CENTER FOR BIOMARKER DISCOVERY
    • PLASMA PROTEOME INSTITUTE
  • 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
  • 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
  • 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

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