Proteomics: An Assesment of Technologies and Commercial Potential

TABLE OF CONTENTS

INTRODUCTION ..................VIII

• STUDY GOALS AND OBJECTIVES ..................VIII
• REASONS FOR DOING THE STUDY ..................VIII
• AUDIENCE FOR THE REPORT ..................IX
• SCOPE AND FORMAT ..................IX
• METHODOLOGY AND INFORMATION SOURCES .................. X
• BCC INFORMATION AND RELATED BCC STUDIES .................. X
• DISCLAIMER ..................XI

EXECUTIVE SUMMARY ..................XII

• OVERVIEW: PROTEOMICS AND THE CURRENT PROTEOMICS MARKET STRUCTURE .................. 1
  • WHAT IS PROTEOMICS? .................. 1
  • TOOLS OF PROTEOMICS .................. 2
    • 2-D ELECTROPHORESIS .................. 2
    • MASS SPECTROSCOPY .................. 3
    • BIOINFORMATICS .................. 4
    OTHER IMPORTANT PROTEOMICS TOOLS .................. 5
    • PROTEIN CHIPS .................. 5
    • CAPILLARY HPLC .................. 6
    USES OF PROTEOMICS TECHNOLOGIES .................. 7
    • IN ACADEMIA .................. 7
    • USES IN DRUG DISCOVERY .................. 7
    • USES IN DIAGNOSTICS .................. 8
    INDUSTRY PERCEPTIONS OF PROTEOMICS AND ITS POTENTIAL .................. 9
  • AN IMPORTANT NOTE ..................10
  GOVERNMENT REGULATIONS ..................12
  • INTRODUCTION ..................12
  • DRUG DISCOVERY ..................13
  • PRECLINICAL TESTING AND SUBMISSION OF AN IND ..................14
  • SUBMISSION OF AN NDA ..................15
  • POST-FDA APPROVAL ..................15
  • CONCLUSIONS ..................16
  • OTHER FINANCIAL ISSUES RELATED TO PHARMACEUTICALS ..................19
  • NEW DRUG APPROVALS ..................20
  MASS SPECTROSCOPY ..................22
  • BASIC THEORY ..................22
  • LIQUID CHROMATOGRAPHY AND MASS SPECTROSCOPY COMBINED ..................22
  • MASS SPECTROSCOPY MARKETS: 2000 TO 2006 ..................23
  • TIME-OF-FLIGHT MASS SPECTROSCOPY ..................27
    • MALDI-TOF ..................28
    • Q-TOF ..................30
    LC-MS: QUADRUPOLE MASS SPECTROSCOPY ..................31
  • LC-ION TRAP MASS SPECTROSCOPY ..................33
  • OTHER DEVELOPMENTS IN THE MASS SPECTROSCOPY BUSINESS ..................33
• PROTEOMICS MARKETS ..................35
  • TWO-DIMENSIONAL ELECTROPHORESIS ..................35
    • OTHER TECHNIQUES FOR SEPARATING PROTEIN MIXTURES ..................38
    MARKET OUTLOOK ..................39
    • SUPPLIERS ..................40
    • Market Leaders in 2-D Electrophoresis ..................43
    CAPILLARY ELECTROPHORESIS (CE) ..................43
    • BACKGROUND ..................44
    • OTHER CE TECHNIQUES FOR ANALYZING PROTEINS ..................47
  • PROTEIN CHIPS ..................50
    • RECENT ADVANCES AND FUTURE OUTLOOK ..................51
  • BIOINFORMATICS ..................54
    • STRUCTURE OF THE BIOINFORMATICS INDUSTRY ..................56
    • BIOINFORMATICS AND PROTEOMICS: DATABASES ..................57
    • BIOINFORMATICS AND PROTEOMICS: SOFTWARE FOR ANALYSIS ..................60
    • CONCLUDING REMARKS ..................61
• PATENT TRENDS ..................63
  • MASS SPECTROSCOPY ..................63
    • PATENTS BY YEAR OF ISSUANCE AND BY TYPE ..................63
    • PATENT ASSIGNEES ..................66
  • CAPILLARY ELECTROPHORESIS PATENT TRENDS ..................70
    • PATENTS BY YEAR OF ISSUANCE AND BY TYPE ..................70
    • PATENT ASSIGNEES ..................76
  • TWO-DIMENSIONAL ELECTROPHORESIS PATENT TRENDS ..................78
    • PATENTS BY YEAR OF ISSUANCE AND BY TYPE ..................78
    • PATENT ASSIGNEES ..................82
• COMPANY PROFILES ..................84
  • MASS SPECTROSCOPY INSTRUMENT SUPPLIERS ..................84
    • AGILENT TECHNOLOGIES, INC. ..................84
    • APPLERA CORPORATION ..................84
    • APPLIED BIOSYSTEMS ..................85
    • BEAR INSTRUMENTS, INC. ..................86
    • GBC SCIENTIFIC EQUIPMENT, PTY. LTD. ..................86
    • HITACHI INSTRUMENTS, INC. ..................87
    • KRATOS ANALYTICAL ..................87
    • MICROMASS ..................87
    • PERKINELMER, INC. ..................88
    • PHENOMENEX ..................89
    • RICHARD SCIENTIFIC, INC. ..................89
    • SHIMADZU SCIENTIFIC INSTRUMENTS ..................90
    • SPARK HOLLAND ..................91
    • THERMO ELECTRON ..................91
    • THERMO SEPARATION PRODUCTS (THERMOQUEST) ..................92
    • VARIAN, INC. ..................92
    • WATERS CORPORATION ..................92
  • 2-D ELECTROPHORESIS OR CAPILLARY ELECTROPHORESIS SUPPLIERS ..................93
    • AMERSHAM PHARMACIA BIOTECH ..................93
    • BIO-RAD LABORATORIES ..................94
    • COMPUGEN ..................95
    • DECODON, GMBH ..................95
    • DIONEX CORPORATION ..................96
    • GENE LOGIC ..................96
    • GENEVA PROTEOMICS ..................97
    • GENOMIC SOLUTIONS, INC. ..................98
    • INVITROGEN ..................98
    • LARGE SCALE BIOLOGY CORPORATION ..................99
    • MICRO-TECH SCIENTIFIC ..................100
    • NONLINEAR DYNAMICS ..................100
    • PROTEOME SYSTEMS LTD. ..................101
    • SCIMAGIX ..................102
    • ZAXIS, INC. ..................102
  • PROTEIN CHIP COMPANIES ..................102
    • APPLERA CORPORATION ..................102
    • BIOSITE, INC. ..................103
    • CELERA GENOMICS ..................104
    • CIPHERGEN BIOSYSTEMS, INC. ..................104
    • GENOMIC SOLUTIONS, INC. ..................105
    • GLAUCUS PROTEOMICS ..................105
    • HTS BIOSYTEMS ..................106
    • HYBRIGENICS SA ..................106
    • ILLUMINA, INC. ..................107
    • LARGE SCALE BIOLOGY CORPORATION ..................108
    • LUMICYTE, INC. ..................108
    • PHYLOS, INC. ..................109
    • PROTIVERIS ..................110
    • SOMALOGIC, INC. ..................110
    • ZYOMYX, INC. ..................111
  • BIOINFORMATICS COMPANIES ..................111
    • AXCELL BIOSCIENCES CORPORATION ..................111
    • CELERA GENOMICS GROUP ..................112
    • GENEVA BIOINFORMATICS ..................112
    • GENEPROT (GENEVA PROTEOMICS) ..................113
    • GENOMIC SOLUTIONS, INC. ..................114
    • HYBRIGENICS SA ..................114
    • INCYTE GENOMICS ..................115
    • INPHARMATICA LTD ..................116
    • INTEGRATIVE PROTEOMICS ..................116
    • MDS PROTEOMICS ..................117
    • MYRIAD GENETICS, INC. ..................117
    • PROTEOME SYSTEMS LTD. ..................118
    • STRUCTURAL BIOINFORMATICS ..................119

LIST OF TABLES

• SUMMARY TABLE: REVENUES FOR SELECTED PROTEOMICS-RELATED PRODUCTS,* WORLDWIDE FORECAST, THROUGH 2006 ..................XII
• 1 PUBLICATIONS CONERNING PROTEOMICS .................. 2
• 2 A SAMPLE OF 2-D ELECTROPHORESIS SUPPLIERS .................. 3
• 3 A SAMPLE OF MASS SPECTROSCOPY SUPPLIERS .................. 4
• 4 A SAMPLE OF COMPANIES INVOLVED IN PROTEOMICS-BIOINFORMATICS .................. 4
• 5 A SAMPLE OF PROTEIN CHIP COMPANIES .................. 6
• 6 IMPORTANT CAPILLARY HPLC COMPANIES .................. 7
• 7 R&D SPENDING IN THE PHARMACEUTICAL INDUSTRY, 1980 TO 2001 ..................17
• 8 DISTRIBUTION OF DRUG RESEARCH COSTS ..................18
• 9 DRUGS APPROVED BY THE FDA, 1993 TO 2000 ..................20
• 10 MASS SPECTROSCOPY EXPENDITURES, THROUGH 2006 ..................23
• 11 MARKET-SPECIFIC MASS SPECTROSCOPY EXPENDITURES, THROUGH 2006 ..................24
• 12 OVERALL MARKET SHARES FOR MASS SPECTROSCOPY, 2000 ..................25
• 13 SELECTED MALDI-TOF MODELS ..................29
• 14 Q-TOF MODELS ..................30
• 15 SELECTED QUADRUPOLE MASS SPECTROMETERS ..................32
• 16 SELECTED ION TRAP MASS SPECTROMETER MODELS ..................33
• 17 2-D GEL ELECTROPHORESIS EXPENDITURES, THROUGH 2006 ..................38
• 18 SELECTED UNITS FOR 2-D ELECTROPHORESIS UNITS* ..................41
• 19 SELECTED SOFTWARE PACKAGES FOR ANALYZING 2-D ELECTROPHORESIS EXPERIMENTS ..................41
• 20 THE CAPILLARY HPLC MARKET, THROUGH 2006 ..................44
• 21 SELECTED MODELS OF AUTOMATED CAPILLARY HPLC EQUIPMENT ..................46
• 22 SELECTED MODELS OF AUTOMATED CAPILLARY ELECTROPHORESIS EQUIPMENT ..................49
• 23 PROJECTIONS FOR PROTEIN CHIP REVENUES, THROUGH 2006 ..................50
• 24 SUPPLIERS OF PROTEIN CHIPS ..................53
• 25 PROJECTIONS FOR BIOINFORMATICS EXPENDITURES, THROUGH 2006 ..................55
• 26 SELECTED COMMERICAL PROTEOMICS DATABASES ..................58
• 27 SELECTED SOFTWARE PACKAGES FOR ANALYZING 2-D ELECTROPHORESIS EXPERIMENTS ..................60
• 28 MASS SPECTROSCOPY PATENTS BY YEAR OF ISSUANCE: 1996 TO JULY 2001 ..................63
• 29 PATENTS BY TECHNOLOGY TYPE, 1996 TO JULY 2001 ..................64
• 30 PATENTS RELATING TO PROTEIN SEQUENCING BY MASS SPECTROSCOPY, 1996 TO JULY 2001 ..................66
• 31 PATENTS BY ASSIGNEE CLASSIFICATION ..................66
• 32 PATENTS BY INSTITUTION, 1996 TO JULY 2001* ..................67
• 33 CAPILLARY ELECTROPHORESIS/MASS SPECTROSCOPY PATENTS ..................68
• 34 MALDI-TOF PATENTS ..................69
• 35 PROTEOMICS-RELATED METHODS/MASS SPECTROSCOPY PATENTS ..................70
• 36 CAPILLARY ELECTROPHORESIS PATENTS BY YEAR OF ISSUANCE, 1996 TO JULY 2001 ..................71
• 37 CAPILLARY ELECTROPHORESIS: APPARATUS AND REAGENTS PATENTS, 1996 TO JULY 2001 ..................72
• 38 CAPILLARY ELECTROPHORESIS: METHODS PATENTS, 1996 TO JULY 2001 ..................74
• 39 CAPILLARY ELECTROPHORESIS PATENTS BY TECHNOLOGY TYPE, 1996 TO JULY 2001 ..................76
• 40 CAPILLARY ELECTROPHORESIS PATENTS BY ASSIGNEE CLASSIFICATION ..................77
• 41 ALL ELECTROPHORESIS PATENTS BY INSTITUTION, 1996 TO JULY 2001* ..................77
• 42 TWO DIMENSIONAL ELECTROPHORESIS PATENTS BY YEAR OF ISSUANCE, 1986 TO JULY 2001 ..................78
• 43 TWO DIMENSIONAL ELECTROPHORESIS: APPARATUS AND REAGENTS PATENTS, 1986 TO JULY 2001 ..................79
• 44 TWO DIMENSIONAL ELECTROPHORESIS: METHODS PATENTS, 1989 TO JULY 2001 ..................81
• 45 PATENTS BY TECHNOLOGY TYPE, 1996 TO JULY 2001 ..................82
• 46 ALL ELECTROPHORESIS PATENTS BY INSTITUTION, 1996 TO JULY 2001* ..................83

LIST OF FIGURES

• SUMMARY FIGURE: REVENUES FOR SELECTED PROTEOMICS-RELATED PRODUCTS,* WORLDWIDE FORECAST, 2000, 2001 AND 2006 ..................XIII
• 1 DRUGS APPROVED BY THE FDA, 1993 TO 2000 ..................21
• 2 MASS SPECTROSCOPY EXPENDITURES, 2000, 2001 AND 2006 ..................24
• 3 OVERALL MARKET SHARES FOR MASS SPECTROSCOPY, 2000 ..................26
• 4 PROTEIN SEPARATION USING 2-D ELECTROPHORESIS ..................36