2008/2009 msppsa series protein expression … · 2016. 11. 16. · resps' familiarity with...

�2008/2009 MSPPSA SERIES

PROTEINEXPRESSION &

PURIFICATION SYSTEMS

AN ANALYSIS OFMARKET SIZE & GROWTH

MARKET SHAREPURCHASE PLANS &

SUPPLIER ASSESSMENT FOR THENORTH AMERICAN LIFE SCIENCE RESEARCH

MARKET

� �ulti-�lient �eport

byPhorTech InternationalSan Carlos, California

February 29, 2008

Copyright 2008 by PhorTech International, 238 Crestview Drive, San Carlos CA 94070. All rights reserved. No material containedin this report may be reproduced in whole or in part without the written permission of the publisher. This report is not intended tobe, and should not be construed as a recommendation for the purchase or sale of any securities mentioned herein. The informationhas been derived from statistical and other sources which we deem reliable but their completeness cannot be guaranteed. Opinionsexpressed herein are based upon our interpretation of available information and are subject to change.

2008/2009 North American MSPPSA Protein Expression & Purification Systems Report

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TABLE OF CONTENTS

I. BACKGROUND...................................................................... 13A. Survey Objectives ............................................................ 14B. Survey Methodology........................................................ 21

II. DEMOGRAPHIC SEGMENTATION......................................... 23#1. Respondent's Involvement with Protein Expression ........ 24#0. Computer Operating Systems & Browser Used ............... 25#91. Segmentation by Organizational Type ............................. 27#92. Segmentation by Job Description .................................... 35#93. Years of Experience with Protein Expression .................... 37#94. Segmentation by Scientific Discipline .............................. 39#95. Core Facilities Providing/Not Providing Services ............. 41#3. Basis for Response: Individual vs. Entire Lab Usage......... 42#4. Researchers in Lab Performing Proteomics Research........ 43

III. MARKET SIZE ANALYSIS ..................................................... 45

#0+. Pop’n Est of North American Rsrchrs Expressing Proteins 46#2. Respondents Use of Protein Expression Systems .............. 49#5. Estimated Annual Spend on Expression Products ............ 53#5A. Estimated Annual Spend on Protein Purificat'n Products 58#7. Protein Expression Expenditure, by Cell System.............. 63#7A. Associated Protein Purification Expenditure, by Product . 68

IV. MARKET SHARE ................................................................. 71

#12. Familiarity with Expressn/Purificatn Product Suppliers ... 72#7+. Protein Expression Product Market Analysis.................... 75#7A+. Protein Purification Product Market Analysis .................. 103

V. PURCHASE PLANS................................................................117

#6. % Change in System Usage over Next 12 Mths ............... 118#6A. % Change in Purificat'n Product Usage, Next 12 Mths... 120

VI. PROTEIN EXPRESSION & PURIFICATION METHODOLOGY .123

#2A. Main Reason for Using Protein Expression Systems......... 124#20. Origins of Protein Expressed............................................ 141#21. Types of Protein Expressed .............................................. 144#29. Required Characteristics of Expressed Proteins ................ 147#30. Post-Translational Modifications Required...................... 150#23. Purification Methods for Expressed Proteins.................... 153#24. Number of Chromatography Steps Performed................. 157#25. Yield vs. Quantity of Protein Required by System............ 159


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#26. Number of Proteins or Variants Expressed Monthly ........ 164

VII. AUTOMATED PROTEIN PURIFICATION SYSTEMS ...............167

#27. Respondents' Usage of Automated Systems ..................... 168#28. Brands & Models of Automated Purification Systems...... 170#31. Downstream Applications for Expressed Proteins ............ 174

VIII. PROKARYOTIC CELL METHODOLOGY .............................179

#80. Throughput of Prokaryotic Preps, per Month.................. 180#81. Prokaryotic Expression Vectors in Use............................. 182#82. Type of Promoter Used Most Often ................................ 185#83. Fusion Tags Used for Purification, Prokaryotic Cells ....... 187#84. Protease Cleavage Enzymes Used Most Frequently .......... 189

IX. MAMMALIAN CELL METHODOLOGY ..................................191

#40. Throughput of Mammalian Preps, per Month................. 192#41. Use of Specific Mammalian Expression Systems .............. 194#42. Expression System Used Most Often ............................... 195#43. Type of Vector Used Most Often .................................... 197#44. Epitope Tags Used Most Often ....................................... 200#45. Generation of Stable Cell Lines for Expression ................ 203#46. Vector or Kit Used to Generate Stable Cell Lines............. 204#47. Products Used to Express Transiently Transfected Cells .. 207

X. INSECT CELL METHODOLOGY.............................................211

#60. Throughput of Insect Preps, per Month .......................... 212#61. Use of Baculovirus for Insect Cell Expression................... 214#62. Type of Baculovirus DNA Used ...................................... 215#63. Baculovirus Transfer Vectors Used Most Often ............... 217#64. Use of Nonlytic Stable Systems........................................ 219#65. Insect Cell Lines Used for Protein Expression .................. 221#66. Fusion Tags Used for Purification, Protns in Insect Cells. 223

XI. YEAST CELL METHODOLOGY.............................................225

#70. Throughput of Yeast Preps, per Month ........................... 226#71. Type of Yeast Strain Used................................................ 228#72. Fusion Tags Used for Purification, Protns in Yeast Cells.. 230

XII. CELL-FREE/IN VITRO EXPRESSION METHODOLOGY..........233

#50. Throughput of Cell-Free/in vitro Preps, per Month......... 234#51. Reason for Using Cell-Free/in vitro Expression Systems... 236#53. Type of Cell-Free Systems Currently in Use .................... 239#53A. Usage of Single vs. Two-Step Procedures ......................... 241#54. Promoters Used Most Often............................................ 242


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#55. Preferred Type of Template for Cell-Free Reactions ........ 244#56. Preferred Template mRNA.............................................. 246#57. Epitope Tags Used Most Often ....................................... 247#58. Preferred Detection Method ............................................ 249#59. Resps Considering Using a HighThroughput Format...... 251#59A. Details Regarding Future High Throughput Usage.......... 252

XIII. SUPPLIER ASSESSMENT ....................................................253

#8. Reasons Given for Protein Expression Product Selection . 254#8A. Reasons Given for Protein Purification Product Selection 279#10. Rejected Protein Expression Brands & Reasons ............... 295#13. Importance of Factors in Supplier Selection Process......... 299#14. Ranked Expression/Purification Supplier Performance .... 302

XIV. FUTURE EXPECTATIONS ..................................................313

#11. Desired Improvements in Protein Expression Products.... 314#11A. Desired Improvements in Expressed Protein Purification. 331

XV. QUESTIONNAIRE...............................................................349


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LIST OF TABLES & GRAPHS

I. BACKGROUND............................................................................................ 13Survey Objectives............................................................................................. 14Survey Methodology ........................................................................................ 20Survey Response Rates ..................................................................................... 20

II. DEMOGRAPHIC SEGMENTATION............................................................... 23Computer Operating Systems Used to Answer Survey Questionnaire............... 24Browser Used to Answer Survey Questionnaire ................................................ 24Distribution by Type of Organization, All Respondents................................... 28Location of Researchers Using Protein Expression Systems, By Org Type ........ 28Distribution by Job Description....................................................................... 35Years of Experience with Protein Expression .................................................... 37Statistical Years of Experience with Protein Expression, By Type of Organizatn 38Distribution by Scientific Discipline, All Respondents ..................................... 39Percent of Resps Working in Core Facilities Providing Protn Exprssn Services . 41Basis for Responses: Individual or Laboratory Usage......................................... 42#Researchers/Lab Expressing/Purifying Protein, Resps Answering for Lab........ 43Statistical # Resrchrs/Lab Involved w/ Protein Expression, by Type of Lab....... 44

III. MARKET SIZE ANALYSIS........................................................................... 45Population Estimate of Life Science Researchers Using Protein Expression....... 47Cell Systems Currently Used for Protein Expression, Share of Mentions .......... 49Cell Systems Currently Used for Protein Expression, Percent of Respondents .. 50Estimated Population of N American Life Science Researchers, by Cell System 51% of Resps Using Cell Systems for Protein Expression, by Organization Type . 51Verbatim Description of Other’ Cell Systems Used for Protein Expression....... 52Statistical Annual Protein Expression Budgets, Individual vs Lab Usage ........... 53Distribution of Annual Protein Expression Budgets, Individual vs Lab Usage... 54Weighted Mean Annual $ Spend/Researcher for Protein Expression Products,. 54Annual N American $ Mkt Size Estimate for Expression Products, .................. 54Statistical Annual Protein Expression Budgets, by Type of Organization .......... 55Share of Annual Protein Expression Budgets, by Type of Organization ............ 56Distribution of Annual Protein Expression Budgets, Major Organization Types 56Statistical Annual Protein Purification Budgets, Individual vs Lab Usage.......... 59Distribution of Annual Protein Purification Budgets, Individual vs Lab Usage . 59Weighted Mean Annual $ Spend/Researcher for Protein Purification Products, 60Annual N American $ Mkt Size Estimate for Purification Products,................. 60Total Annual N American $ Mkt Size Estimate for Expression & Purification, 60Statistical Annual Protein Purification Budgets, by Type of Organization ........ 60Share of Annual Protein Purification Budgets, by Type of Organization .......... 61Distribution of Annual Protein Purificat'n Budgets, Major Organization Types 61Mean Percent of Budget Spent by Cell System, Expression Audit..................... 63Share of Mentions by Cell System Expression Audit......................................... 64Share of Dollar Spend by Cell System, Expression Audit.................................. 65Mean Annual Dollar Spend per Entry by Cell System, Expression Audit.......... 66Annual N American $ Mkt Size Estimate for Expression, by Cell System, ........ 66Statistical Annual $ Spend/Rschr by Cell System, Expression Audit ................. 67Mean Percent of Budget Spent by Type of Product, Purification Audit............ 69Annual Dollar Spend for Associated Purification Products, by Category........... 69Annual N American $ Mkt Size Estimate for Purification, by Category,........... 70


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Statistical Annual $ Spend/Resp for Purification Products, by Category ........... 70Statistical Annual $ Spend/Rschr for Purification Products, by Category.......... 70

IV. MARKET SHARE ....................................................................................... 71Resps' Familiarity with Suppliers of Expression/Purification Products .............. 73Verbatim Descriptions of 'Other' Familiar Suppliers for Express'n/Purificat'n.. 74Mean Percent of Budget Spent by Cell System, Expression Audit..................... 76Summary of Share of Mentions & $ Mkt Share for Expression, by Cell System 77Statistical Annual $ Spend/Resp for Expression Products, by Cell System ........ 78Comm'l Suppliers’ Share of Mentions, Protein Expression Product Audit........ 78Comm'l Suppliers’ $ Market Share, Protein Expression Product Audit............. 80% of Resps Purchasing Expression Products from Major Suppliers................... 80Mean Spend per Entry, Major Suppliers of Protein Expression Products.......... 81Protein Expression Product Suppliers in the 'Other' Category.......................... 82

Mammalian Protein Expression Systems........................................................ 83Mean, Median & Mode Annual Spend per Respondent................................... 83Comm'l Suppliers’ Share of Mentions, Mammalian Expression Products ......... 84Comm'l Suppliers’ $ Market Share, Mammalian Expression Products.............. 85Mean Spend per Entry, Major Suppliers of Mammalian Protn Expressn Prods. 85Mammalian Protein Expression Suppliers in the 'Other' Category ................... 85% of Resps Purchasing Mammalian Express'n Prods from Major Suppliers ...... 87

Prokaryotic Protein Expression Systems ........................................................ 87Mean, Median & Mode Annual Spend per Respondent................................... 87Comm'l Suppliers’ Share of Mentions, Prokaryotic Expression Products .......... 88Comm'l Suppliers’ $ Market Share, Prokaryotic Expression Products............... 89Mean Spend per Entry, Major Suppliers of Prokaryotic Protn Expressn Prods.. 89Prokaryotic Protein Expression Suppliers in the 'Other' Category .................... 89% of Resps Purchasing Prokaryotic Expression Products from Major Suppliers 90

Insect Protein Expression Systems ................................................................. 91Mean, Median & Mode Annual Spend per Respondent................................... 91Comm'l Suppliers’ Share of Mentions, Insect Expression Products................... 92Comm'l Suppliers’ $ Market Share, Insect Expression Products ....................... 92Mean Spend per Entry, Major Suppliers of Insect Protein Expression Products 93Insect Protein Expression Suppliers in the 'Other' Category ............................. 93% of Resps Purchasing Insect Expression Products from Major Suppliers......... 94

Yeast Protein Expression Systems .................................................................. 94Mean, Median & Mode Annual Spend per Respondent................................... 94Mean Spend per Entry, Major Suppliers of Yeast Protein Expression Products . 94Comm'l Suppliers’ Share of Mentions, Yeast Expression Products.................... 95Comm'l Suppliers’ $ Market Share, Yeast Expression Products ........................ 95Yeast Protein Expression Suppliers in the 'Other' Category .............................. 96% of Resps Purchasing Yeast Express'n Prods from Major Suppliers................. 96

Cell-Free/in vitro Protein Expression Systems................................................ 97Mean, Median & Mode Annual Spend per Respondent................................... 97Comm'l Suppliers’ Share of Mentions, Cell-Free/in vitro Expression................ 97Comm'l Suppliers’ $ Market Share, Cell-Free/in vitro Expression .................... 98Mean Spend per Entry, Major Suppliers of Cell-Free Protn Express'n Products 98Cell-Free (in vitro) Protein Expression Suppliers in the 'Other' Category ......... 98% of Resps Purchasing Cell-Free/in vitro Express'n Prods, Major Suppliers ..... 99


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Plant Protein Expression Systems .................................................................. 99Mean, Median & Mode Annual Spend per Respondent................................... 99Mean Spend per Entry, Major Suppliers of Plant Protein Expression Products. 99Comm'l Suppliers’ Share of Mentions, Plant Expression Products.................... 100Comm'l Suppliers’ $ Market Share, Plant Expression Products ........................ 100

Other Protein Expression Systems ................................................................. 100Summary of Suppliers' Mkt Shares for Exprssn Products for 'Other' Systems... 101

Annual N American $ Mkt Size Estimates/Leading Comml Suppliers, by Systm 102

Classes of Protein Purification Products ........................................................ 103Mean Percent of Budget Spent by Type of Product, Purification Audit............ 104% of Purification Budget Spent on Lysis Systems, Instruments & Columns ..... 104Statistical Annual $ Spend for Purification Products, by Product Category ...... 105Distribution of Annual Spend on Lysis Systems, Instruments & Columns ....... 105Statistical Annual $ Spend/Rschr for Purification Products, by Prod Category . 106

Columns Used to Purify Expressed Proteins .................................................. 106Mean, Median & Mode Annual Spend per Respondent for Columns .............. 106Comm'l Suppliers’ Share of Mentions, Columns for Protein Purification......... 107Comm'l Suppliers’ $ Market Share, Columns for Protein Purification ............. 107% of Resps Purchasing Columns from Major Suppliers.................................... 108Suppliers of Columns for Protein Purification in the 'Other' Category............. 108

Instrumentation Used to Purify Expressed Proteins....................................... 109Mean, Median & Mode Annual Spend per Respondent for Instrumentation ... 109Comm'l Suppliers’ Share of Mentions, Instrumentation for Protn Purification 110Comm'l Suppliers’ $ Market Share, Instrumentation for Protn Purification ..... 110Mean Spend per Entry, Instrumentation for Protein Purification ..................... 111Suppliers of Instrumentation for Protein Purification in the 'Other' Category.. 111% Resps Purchasing Protn Purificatn Instrumentation from Major Suppliers ... 112

Lysis Systems Used to Purify Expressed Proteins ........................................... 112Mean, Median & Mode Annual Spend per Respondent for Lysis Systems........ 112Comm'l Suppliers’ Share of Mentions, Lysis Systems for Protein Purification .. 113Comm'l Suppliers’ $ Market Share, Lysis Systems for Protein Purification ....... 113Mean Spend per Entry, Major Suppliers of Lysis Systems for Protn Purification 114Suppliers of Lysis Systems for Protein Purification in the 'Other' Category ...... 114% Resps Purchasing Lysis Systems for Protn Purificat'n from Major Suppliers . 115

Annual N American $ Mkt Size Estimates/Leading Comm'l Suppliers, by Prod 116

V. PURCHASE PLANS...................................................................................... 117Forecast Change in Protein Expression Systems, Over the Coming 12 Months 118Weighted Mean Change in Expression System Usage for the Next 12 Mths..... 1192009 Sales Projections for Protein Expression Products.................................... 119Forecast Change in Purification Product Usage, Over the Coming 12 Mths .... 120Weighted Mean Change in Purification Product Usage for the Next 12 Mths.. 1212009 Sales Projection for Associated Protein Purification Products .................. 1212009 Combined Sales Projection for Protein Expression & Purification Prods . 121

VI. PROTEIN EXPRESSION & PURIFICATION METHODOLOGY ....................... 123

Verbatim Descriptions of Reasons for Using Protein Expression Systems ......... 124


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Frequently Mentioned Reasons for Selecting a Cell System for Expression ....... 139Average # of Different Protein Origins Expressed/Resp .................................... 141Origins of Proteins Used for Expression, Share of Mentions............................. 141Origins of Proteins Used for Expression, % Resps Expressing Each .................. 142Verbatim Descriptions of Unlisted Origins of Proteins Used for Expression..... 142Type of Proteins Used for Expression, Average # of Responses ......................... 144Type of Proteins Used for Expression, Share of Mentions ................................ 144Types of Proteins Used for Expression, % Resps Utilizing Each ....................... 145Verbatim Descriptions of Unlisted Types of Proteins Used for Expression ....... 145Average # of Required Characteristics of Expressed Proteins/Resp .................... 147Required Characteristics of Expressed Proteins, Share of Mentions................... 147Characteristics of Expressed Proteins Required by Respondents ....................... 148Most Common Combinations, Characteristics Required of Expressed Proteins 149'Other' Required Characteristics of Expressed Proteins..................................... 149Required Post-Translational Modifications, Share of Mentions ........................ 151Required Post-Translational Modifications, Percent of Respondents ................ 151Verbatim Descriptions of 'Other' Post-Translational Modifications ................. 152Average Number of Protein Purification Methods Used/Resp .......................... 153Current Methods of Protein Purification, Share of Mentions ........................... 153Current Methods of Protein Purification, % Resps Utilizing Each ................... 154Five Most Common Purification Method Combinations & # of Users ............ 154Verbatim Descriptions of 'Other' Methods of Protein Purification................... 155Mean, Median & Mode # of Chromatography Steps to Purify Proteins ........... 157Number of Chromatography Steps Performed to Purify Proteins ..................... 157Mean, Median & Mode Protein Yield, All Cell Systems................................... 159Protein Yield Typically Obtained, All Cell Systems .......................................... 160Statistical Yield of Expressed Proteins (in Mg), by Cell System......................... 160Protein Yield Typically Obtained (Prokaryotic, Mammalian, Insect & Yeast)... 161Mean, Median & Mode Quantity of Expressed Protn Required, All Systems ... 161Quantity of Expressed Protein Required, All Cell Systems................................ 162Statistical Quantity of Expressed Protein Required (in Mg), By Cell System .... 162Quantity of Expressed Protein Required, (Prokaryotic, Mammln, Insect, Yeast) 163Comparison of Yield and Quantity Required, Share of Mentions ..................... 163Number of Proteins or Variants Expressed per Month ..................................... 164

VII. AUTOMATED PROTEIN PURIFICATION SYSTEMS ..................................... 167

Auto Protein Purification Systems Usage, Current Usage & Future Plans ........ 168Auto Protein Purification Current & Future Users, by Type of Organization... 169Automated Protein Purification Systems Currently in Use ............................... 170Unit Shares for Comm'l Suppliers, Automated Protein Purification Systems.... 172Year of Acquisition, Automated Protein Purification Systems........................... 172Verbatim Descriptions of Downstream Applications for Expressed Proteins ..... 174

VIII. PROKARYOTIC CELL METHODOLOGY ................................................... 179

Resps' Throughput of Prokaryotic Preps/Month, by Basis of Response ............ 180Average Number of Prokaryotic Preps/Month, Individuals vs. Entire Labs ....... 181Extrapolated Throughput of Prokaryotic Preps/Month in North America........ 181Prokaryotic Expression Vectors Currently in Use ............................................. 182Verbatim Descriptions of ‘Other’ Prokaryotic Expression Systems.................... 183Promoter Used Most Often with Prokaryotic Cell Systems .............................. 186Verbatim Descriptions of 'Other' Promoters Used for Prokaryotic Expression.. 186Fusion Tags Used Most Often, Protein Purificatn/Detctn in Prokaryotic Cells 187


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‘Other’ Fusion Tags Used Often, Purif/Detectn of Protns in Prokaryotic Cells 188Protease Cleavage Enzymes Frequently Used with Prokaryotic Cell Systems..... 189'Other' Protease Cleavage Enzymes Used Most Frequently, Prokaryotic Exprss 190

IX. MAMMALIAN CELL METHODOLOGY ........................................................ 191

Average Number of Mammalian Preps/Month, Individuals vs. Entire Labs ...... 192Resps' Throughput of Mammalian Preps/Month, by Basis of Response ........... 193Extrapolated Throughput of Mammalian Preps/Month in North America....... 193Usage of Specific Expressn Systems Used to Produce Protns in Mammln Cells 194Mammalian Expression Systems Used Most Often........................................... 195Verbatim Description of ‘Other’ Mammalian Expression Systems.................... 196Vectors Used Most Frequently, Mammalian Cell Systems, % of Resps............. 197Resps Purchasing Vectors from Suppliers, Mammalian Cell Systems, % Resps . 199Verbatim Description of ‘Other’ Expressn Vectors, Used w/ Mammln Cell Sys 199Epitope Tags Used Most Frequently, Percent of Respondents .......................... 201Verbatim Description of ‘Other’ Epitope Tags for Detection/Analysis Protns .. 201Verbatim Descriptn of Expressn Vectors/Kits Used to Express Mammln Prtns. 204Verbatim Description of ‘Other’ Expressn Vectors/Transient Mammln Expr ... 207

X. INSECT CELL METHODOLOGY .................................................................. 211

Mean, Median & Mode Preps/Month per Respondent .................................... 212Resps' Throughput of Insect Preps/Month, by Basis of Response ..................... 212Average Number of Insect Preps/Month, Individuals vs. Entire Labs................ 213Extrapolated Throughput of Insect Preps/Month in North America ................ 213Usage of Baculovirus to Produce Proteins in Insect Cells.................................. 214Type of Baculovirus DNA Used to Generate Recombinant Virus..................... 215Verbatim Descriptions of 'Other' Baculovirus DNA Used to Generate Virus ... 216Type of Baculovirus Transfer Vectors Used Most Often, Percent of Resps ....... 217Verbatim Descriptions of 'Other' Baculovirus Transfer Vectors........................ 218Use of Nonlytic Stable Systems ........................................................................ 219Type of Insect Cell Lines Used to Produce Recombinant Proteins.................... 221Fusion Tags Used Most Often, Protein Purification in Insect Cells .................. 223

XI. YEAST CELL METHODOLOGY................................................................... 225

Average Number of Yeast Preps/Month, Individuals vs. Entire Labs................. 226Resps' Throughput of Yeast Preps/Month, by Basis of Response ...................... 227Extrapolated Throughput of Yeast Preps/Month in North America.................. 227Strains of Yeast Used to Produce Recombinant Proteins................................... 228Verbatim Descriptions of 'Other' Yeast Strains Used Most Often .................... 229Fusion Tags Used Most Often, Protein Purification in Yeast Cells ................... 230Fusion Tags Used Most Often, Prokaryotic vs. Insect vs. Yeast Cells ................ 231

XII CELL-FREE/IN VITRO EXPRESSION METHODOLOGY ................................ 233

Mean Preps/Month per Respondent ................................................................ 234Average Number of Cell-Free Preps/Mth, Individuals vs Entire Labs................ 234Resps' Throughput of Cell-Free/in vitro Preps/Month, by Basis of Response ... 235Extrapolated Throughput of Cell-Free/in vitro Preps/Month ........................... 235Extrapolated Throughput of Cell-Free/in vitro Preps/Month, by Cell System .. 235Reasons for Selecting Cell-Free/in vitro Expression System............................... 236Type of Cell-Free Systems Currently Used for Protein Expression.................... 239Preferred Procedure for Cell-Free Protein Expression ....................................... 241


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Promoters Used Most Often, Cell-Free Expression........................................... 242Type of Template Preferred for Cell-Free Translation Reactions ...................... 244Respondents' Preferred Template mRNA for Cell-Free Translation Reactions.. 246Epitope Tags Used Most Frequently, Cell-Free Systems, % of Respondents ..... 247Type of Detection Preferred, Cell-Free in vitro Translated Proteins.................. 249Resps Considering High Throughput, 96/384 Well Cell-Free Expression ........ 251Additional Details Regarding Movement to High Throughput Format Usasge. 252

XIII. SUPPLIER ASSESSMENT.......................................................................... 253Verbatim Reasons for Selecting Protein Expression Product Suppliers.............. 254Most Frequently Mentioned Reasons for Selecting Expressn Prod Suppliers..... 277Verbatim Reasons for Protein Expression Brand Selection................................ 279Most Frequently Mentioned Reasons for Selecting Purification Prod Suppliers 293Refusal to Buy From Specific Suppliers, Protein Expression/Purification Prods 295Satisfaction Rates for Major Suppliers .............................................................. 296Satisfaction Rates and 65% Confidence Levels for Major Suppliers .................. 297Verbatim Reasons for Not Purchasing Specific Brands ..................................... 298Importance of Factors-Supplier Selection, Resps Rating 1-5 on a 10-Pt Scale ... 300Importance of Factors in Selecting Protn Expressn/Purificatn System Supplier. 301Ranked Suppliers’ Performance: Reliable Performance ..................................... 303Ranked Suppliers’ Performance: Consistent Quality......................................... 304Ranked Suppliers’ Performance: Ease of Use .................................................... 304Ranked Suppliers’ Performance: Previous Experience ....................................... 305Ranked Suppliers’ Performance: Best Value for Money .................................... 306Ranked Suppliers’ Performance: Procedures to Minimize Hands-On Time...... 306Ranked Suppliers’ Performance: Colleague's Recommendation ........................ 307Ranked Suppliers’ Performance: Reputation of Supplier................................... 307Ranked Suppliers’ Performance: Availability/Ease of Ordering ......................... 309Ranked Suppliers’ Performance: Literature Reference....................................... 309Computed Total Points for Criteria Derived from Mean Importance............... 310Weighted Score for Protein Expression & Protein Purification Suppliers.......... 311

XIV. FUTURE EXPECTATIONS ........................................................................ 313Suggested Improvements in Protein Expression Products ................................. 314Frequently Mentioned Improvements, Protein Expression Products................. 328Suggested Improvements in Products Used for Protein Purification ................. 331Frequently Mentioned Improvements, Protein Purification Products ............... 347

XV. QUESTIONNAIRE..................................................................................... 349


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I. BACKGROUND


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A. SURVEY OBJECTIVES

The purpose of this survey was to provide our clients with an analysis of thecurrent North American market for recombinant protein expression systemsincluding a detailed examination of the associated protein purification. Thisreport will focus on the products used and the procedures in place, alongwith the attitudes and expectations of researchers regarding recombinantprotein expression of six different cell systems.

The survey was Web-based, at a location on our Web site made known torespondents through an email invitation. The surveying was blind, with noreference made to any of our clients. To encourage respondents to expressthemselves freely, the survey was anonymous, and made frequent use of open-ended questions.

Several demographic screens were used to characterize respondents. Theseinclude the type of organization and scientific discipline, job description, typeof laboratory (core facility providing protein expression services, notproviding these services or not a core facility), and the years of experiencewith protein expression systems.

Early on in the survey, respondents were asked whether they currently userecombinant protein expression systems in their work. Respondentsanswering negatively were automatically screened out of the survey and theirunique user ID was invalidated to prohibit restarting the survey, as they werenot qualified to continue.

Researchers answering this question affirmatively were then asked to providethe basis for their responses from two options, either their individual work orthe combined work of their entire laboratory. Those answering on behalf oftheir lab were queried as to the number of researchers currently involved withprotein expression and subsequent purification, and also covered by thelaboratory’s budget.

Next, respondents were directed to indicate which of six cell systems arecurrently being used in the laboratory for protein expression. Possibleresponses include mammalian, insect, yeast, prokaryotic, cell-free, plant, oralternately, an optional ‘other’ category in which respondents could provide abrief description of the unlisted cell system. They were then asked to describethe main reason these systems were chosen and to estimate the averageexpenditure per year for recombinant protein expression products includingexpression kits and vectors plus associated nucleic acid purification, hoststrains, and cell culture media. They were also asked what percent change inusage of these systems is anticipated over the coming 12 months.


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Separately, respondents were asked to provide the current annual spend onassociated protein purification products including downstream lysis,columns, instrumentation, as well as any other products. They were alsoasked to indicate the percent change in the usage of protein purification ofexpressed proteins which they foresee in the coming 12 months.

These researchers were then directed to provide further details about theircurrent spend on protein expression products, identifying the cell system,major suppliers and the percent of the total expression budget which eachrepresents. Respondents were also queried as to the reason behind purchasingthese brands of protein expression products and to suggest improvements tospecific protein expression products.

Similarly, respondents were also asked to write-in the major supplier(s) andpercent of the total purification budget spend for each of three purificationproduct classes: columns, lysis systems and instrumentation. They were alsoasked to indicate the reason for selecting these products, in their own words,and describe any improvements that come to mind.

A single query measuring dissatisfaction with these suppliers askedrespondents to indicate if there were any companies from which they refuseto purchase. Those answering affirmatively were asked to identify the brandand explain the reason behind their responses.

The next question asks respondents to select the suppliers from analphabetical list of 24 expression/purification product companies that theyrecognize, either because their products are used on a regular basis or theresearcher is familiar with their offerings. This list includes both instrumentsuppliers and reagent companies.

Using a ten point scale, respondents were then asked to rate the importanceof 10 different factors when selecting a protein expression or purificationproduct supplier. These included value for money, procedures to minimizehands-on time, literature references, a colleague's recommendation, previousexperience, ease of use, availability/ease of ordering, reliable performance,consistent quality and the reputation of the supplier.

For up to five ‘important’ factors (identified as those rated above five on theten point scale), respondents then indicated which of the suppliers they arefamiliar with (according to their earlier response) ranked the highestregarding each factor. Using this method, researchers rank only familiarsuppliers for a random selection of those criteria which are most important tothem.

The next series of questions addresses respondents’ protein expression andsubsequent purification, beginning with several multiple choice questionsregarding the origin of proteins used for expression, the types of proteins


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being expressed, the characteristics and post-translational modificationswhich expressed proteins need to have, and the methods used forpurification. More specifically, researchers are also asked to provide thenumber of chromatographic steps it typically takes to purify the protein ofinterest satisfactorily. The number of proteins or variants expressed on amonthly basis is also measured.

Going into greater detail, this section also contains a modified audit in whichrespondents indicate the typical yield of proteins and the quantity ofexpressed protein (in milligrams) typically required for each of up to threedifferent expression systems.

Respondents are then asked to indicate whether they currently use anautomated protein purification system or plan to add this capability withinthe next 12 months. Current users specify whether these systems are usedwith larger-scale preps or for small samples in a high throughput format andare requested to provide the brand, model and year of acquisition of thesystem in their laboratory. In their own words, a single additional query asksfor a description of any downstream applications utilizing expressed proteins.

The remainder of the survey is divided into sections, each containing moredetailed questions about one of the six cell systems. The first of these sectionsconsists of eleven questions addressed to researchers working with cell-fee orin-vitro expression systems. These respondents are asked to indicate the totalnumber of cell-free (in-vitro) preps performed on a monthly basis and toexplain the primary reason(s) for using this expression system in their ownwords. Further details of this lab work are derived from a series of multiplechoice questions. The first asks respondents to identify cell-free system(s)currently being used for protein expression (including human, wheat germ,insect, E. coli, rabbit reticulocyte, fungal/yeast or other). This is immediatelyfollowed by a query examining respondents’ preference for single stepprocedures (transcription coupled to translation in the reaction) or a two-stepprocedure (in which mRNA is transcribed in a separate reaction and thenadded to the translation mix). Other characteristics identified are frequentlyused promoters, the preferred type of template for cell-free translationreactions, the preferred template mRNA, epitope tags used most frequentlyfor purification, detection and analysis of recombinant proteins from cell-freesystems, and also, detection systems preferred for in vitro translated proteins.The final two queries asks respondents to indicate whether they areconsidering moving into a high-throughput cell-free expression system (with96 or 384 wells format), and if so, to provide additional information, such asthe anticipated time-frame for this change, likely suppliers and theanticipated throughput.

Respondents using prokaryotic expression systems are directed to answer aseries of five questions. As for all systems, these researchers are first asked to


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estimate the monthly throughput of prokaryotic preps. Four additionalmultiple choice questions ask these researchers to indicate the prokaryoticexpression systems vector(s) currently in use, the promoter(s) used mostoften, the fusion tags used for the purification or detection of recombinantproteins in prokaryotic cells, and the most common protease cleavageenzymes. For each of these four questions, respondents are provided withcommon responses along with two open-ended responses in which they canwrite-in any unlisted options.

The next three questions are addressed to respondents working with yeastexpression systems. After an initial query requesting the average number ofyeast expression preps performed per month, respondents are also asked toindicate the strains of yeast used to produce recombinant proteins and thefusion tags currently used to purify these expressed proteins.

Respondents currently working with insect expression systems are then askedto indicate how many insect expression preps are performed in their lab on amonthly basis, and to provide a yes/no response regarding whether they usebaculovirus to produce recombinant proteins in insect cells, or use directtransformation of these cells. Those using baculovirus in their work are alsoasked to identify the type(s) of baculovirus DNA used to generate arecombinant virus and the baculovirus transfer vectors used most frequently.

All researchers working with insect expression systems are also asked toindicate the insect cell lines currently used to produce recombinant proteins(from four options plus an open-ended ‘other’ category), and the fusion tagsused to purify these recombinant proteins (from a list of 12 commonresponses plus two open-ended responses). In addition, these researchers arequeried about which nonlytic stable systems are used to express recombinantproteins in insect cells.

Consistent with each of the other cell systems covered so far, researchersinvolved with mammalian expression systems are also queried as to theiraverage monthly throughput of preps using this system. The second queryasks for a yes/no response regarding respondents’ use of specific expressionsystems for production of proteins in these cells. The next three multiple-choice questions were designed to pinpoint the expression systems used mostfrequently with these cells, common types of vectors and frequently usedepitope tags for detection and analysis of recombinant proteins inmammalian cells. Subsequently, respondents were asked to indicate whetherthey generate stable cell lines for protein expression, and to describe theexpression vector or kit currently used, in their own words. Finally, ifproteins are produced from transiently transfected mammalian cells,respondents were asked to identify the expression vector or expression kit,and transfection agent currently in use.


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Major objectives of this survey were to determine the present market size andshare of expenditure for major suppliers of protein expression products andprotein purification products in general, and for each cell system. Customersatisfaction with these suppliers will also be measured, as will anticipated nearfuture usage of this technique. Finally, specific characteristics of respondent’scurrent usage of each cell system is examined.

The audits should permit the evaluation of our clients’ present marketpositions, identify marketing strengths and weaknesses, and suggest strategiesto develop or improve sustainable competitive advantage.

To better accomplish the survey objectives, a number of programmed featureswere employed. To speed respondents through this survey, skip patterns wereprogrammed into the questionnaire. For example, respondents were asked toprovide the number of researchers working with protein expression orpurification systems if they indicated that they were answering the survey fortheir entire laboratory. Also, researchers who were not qualified to respond tothis survey due to lack of involvement in this area were skipped out of thesurvey. Most importantly, this feature directed respondents working witheach cell system to the appropriate section(s) containing queries related to thecharacteristics of those systems.

Constructed lists were also employed for several questions to simplify andpersonalize the survey based upon responses to earlier questions. For example,in Question #12, respondents were asked to indicate suppliers which they arefamiliar with, and in Question #13, identify the importance of a variety ofcriteria when considering supplier selection. In the subsequent question, #14,only criteria considered to be important (earning a rating of 6 or higher) wereshown and the pull-down menu of suppliers showed only companies familiarto the respondent.

Tailored questions were used to imprint the basis respondents used to answerthe survey. In Question #3, respondents were asked whether they wouldanswer the survey based upon their own personal usage or based on thecombined usage of their laboratory. Depending upon their answer,subsequent questions were worded either ‘your individual usage’ or ‘yourlaboratory’s usage’.

This report is the first 2008/2009 study in a growing series of market researchanalyses that began in 1993. We plan to continue the series, adding titles andalternating between North American and international markets, dependingupon our clients’ suggestions and support.

The series of three reports in the 2007/2008 series covering segments of theNorth American life science research market are entitled:


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Molecular Biology Reagent Systems, Volume 1Proteomics Research, Volume 1 and

Proteomics Research, Volume 2.

The two reports in the 2006/2007 series which have been released cover theNorth American market for

DNA Amplification InstrumentationDNA Amplification Reagents & Methodology

The three reports published in the 2004/2005 series cover the U.S. marketfor:

DNA Sequencing & Sequencing ServicesElectrophoretic Equipment & Reagents and

HPLC Columns in the Life Sciences.

In addition, a single report examining the European market covers the:

Microarray Market Analysis (including Arrayers, Scanners and Microarrays).

Reports published in the 2003/2004 series cover the following U.S. topics:

Molecular Biology Reagent Systems, Vol. 1Molecular Biology Reagent Systems, Vol. 2

Protein Expression SystemsProteomics Research, Volume 1 (Sample Prep & 2-D)

Proteomics Research, Volume 2 (Mass Spec & Protein Microarrays).

Reports released in the 2002/2003 series include the following U.S. topics:

DNA Amplification InstrumentationDNA Amplification Reagents & Methodology

Microplate Reader & Equipment Market

Topics in the U.S. series published in 2001/2002 include:

Electrophoretic Instrumentation & ReagentsMolecular Biology Reagent Systems, Vol. 2

This series also includes the following reports covering international markets:

Densitometers & Image Analysis in EuropeDNA Sequencing in the Far East.

The 2000/2001 series covered the following three reports:


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U.S. DNA AmplificationU.S. Molecular Biology Reagent Systems, Vol. 1

Molecular Biology Reagent Systems, Vol. 1 in the Far East.

In the 1999/2000 series, we have released three reports examining thefollowing markets. These are:

Microplate Equipment in EuropeDNA Sequencing in the U.S.

Monoclonal Antibodies in the U.S.

The following nine titles have been released in the series for 1998/1999:

Cell & Tissue Culture in the U.S.Cytokines & Growth Factors in the U.S.

DNA Amplification in the Far EastDNA Sequencing in Europe

Electrophoretic Gel Media in EuropeHPLC in the Life Sciences in the U.S.

Molecular Biology Reagent Systems, Vol. 1Molecular Biology Reagent Systems, Vol. 2 in the Far East

Protein Expression Systems in the U.S.

The following titles have been released in the U.S. series for 1997/8:

DNA SequencingMolecular Biology Reagent Systems, Vol. 1Molecular Biology Reagent Systems, Vol. 2

Molecular Diagnostics.

Clients are reminded that additional copies of any of these reports that havebeen purchased in the past are available at a modest cost. Please contact us forfurther details. Those wishing to know publication dates for any of thesereports, or wanting to read summaries of the 72+ reports in this series areinvited to visit our Web site at: www.phortech.com.


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B. SURVEY METHODOLOGY

E-mail invitations to take part in the survey were sent to 12,928 NorthAmerican life science researchers from a single source, the PhorTech panel.The worldwide PhorTech panel consists of 50,000+ life science researchers.These were sent out in small batches from December 10th, 2007 to January7th, 2008.

A total of 1,768 email messages were returned as undeliverable. Thiscorresponds to an undeliverable rate of 13.7%. By deducting this from theoutbound invitations, we calculate that a total of 11,160 U.S., Canadian andMexican life science researchers received invitations to participate in thesurvey.

The survey was closed on January 8th, by which time we had received a totalof 545 responses (including 405 completed responses and 140 partialresponses. This exceeded our original target of 400 completed returns.

A large number, totaling 750 researchers, equivalent to 6.7% of thosereceiving an invitation, indicated that they were willing to take part in thissurvey by opening the questionnaire. However, 63 of these didn’t answer anyquestions. A further 75 attested in Question #1 that they were not involvedwith protein expression and purification and were therefore disqualified fromcontinuing. An additional 67 entries contained responses to the first fewquestions at most, and did not provide any budget figures. While these havebeen excluded from this dataset, incomplete responses from a further 140researchers have been imported into this data set. Although these did notfinish the questionnaire, they do provide useful information, and expand thebasis (to 545 respondents) for our analysis of the early questions which definegeneral characteristics of the population of protein expression andpurification users as a whole.

The questionnaires were anonymous, using a combination of tabular entry,check-offs, and open-ended probes. However, almost all respondents dididentify themselves by filling in the prize entry form. This makes it possiblefor us to double-check the responses to any questions by telephoningrespondents, improving the overall confidence in the data. We did notobserve any survey fatigue in this questionnaire, and felt that respondentsspent considerable time explaining their positions on the open-endedquestions.

For all 545 complete and partial responses, the overall statistical results thatwill be presented in the final report will be accurate to within ± 4.2percentage points at the 95% confidence level. Results based on the 405completed responses only are accurate to within ± 4.9 percentage points atthe 95% confidence level.


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In our experience, 95% confidence levels are appropriate primarily forscientific experiments. Most business people making decisions are content tobe right more often than they are wrong. In this case, a 65% confidence level,(in which you would be right twice as often as you would be wrong) is moreappropriate. Conveniently, 65% confidence levels are nearly exactly one halfthe size of the 95% level, thus our 65% levels would be ± 2.1% for all 545respondents, and ± 2.4% for the 405 respondents completing the surveyquestionnaire.

According to the binomial distribution theory, these values are valid when themeasured event has about a 50% probability. When the measured event isconsiderably more rare than this, the corresponding confidence intervals getsmaller. On the other hand, these confidence intervals are valid for answersbased upon the complete pool of respondents. When analyzing data for agroup that includes only a small segment of respondents, the answers are lesscertain and confidence intervals are correspondingly larger.

In this report, we will calculate more exact individual confidence intervalswhen appropriate. In our comments, we will note whether given differencesare significant at either the 65% or 95% level. To aid our client indetermining the appropriate confidence interval for various combinations ofsample size and measurements, we have created the following table. Just readthe closest percentage on the left and find the closest sample size column. Theintersection will show the confidence interval for that combination. Forexample, a measured 35% value with a sample size of 200 has a 95%confidence interval of ± 6.6%.

95% Confidence Intervals for Various Percentages & Sample SizesPercent n=10 n=20 n=50 n=100 n=200 n=500 n=1000

5% ±13.5% ±9.6% ±6.0% ±4.3% ±3.0% ±1.9% ±1.4%10% ±18.6% ±13.1% ±8.3% ±5.9% ±4.2% ±2.6% ±1.9%20% ±24.8% ±17.5% ±11.1% ±7.8% ±5.5% ±3.5% ±2.5%35% ±29.6% ±20.9% ±13.2% ±9.3% ±6.6% ±4.2% ±3.0%50% ±31.0% ±21.9% ±13.9% ±9.8% ±6.9% ±4.4% ±3.1%65% ±29.6% ±20.9% ±13.2% ±9.3% ±6.6% ±4.2% ±3.0%80% ±24.8% ±17.5% ±11.1% ±7.8% ±5.5% ±3.5% ±2.5%90% ±18.6% ±13.1% ±8.3% ±5.9% ±4.2% ±2.6% ±1.9%95% ±13.5% ±9.6% ±6.0% ±4.3% ±3.0% ±1.9% ±1.4%


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II. DEMOGRAPHICSEGMENTATION


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QUESTION 1. Question:Do you currently use any recombinant protein expression systems in yourwork?: Yes, we currently use recombinant protein expression systems; No, wedo not use recombinant protein expression systems.

Rationale:This serves as a primary screening question identifying whether a researcher iscurrently working in this area. Respondents answering this questionnegatively are directed out of the questionnaire by the survey engine, as theyare not qualified to continue.

Results:Since only researchers who are currently working with protein expressionsystems were included in this analysis, all 545 respondents included in thisdataset answered this question affirmatively.


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QUESTION 0. Question:Our latest software program permits us to identify two primary characteristicsof the computers respondents are using, the operating system and browser.

Rationale:We provide a brief summary of this information giving clients a general ideaof the type of computer and browser which these researchers have access to.

Results:First, we present the distribution of the operating system run on thecomputers our respondents used to answer the survey. These are sorted indescending order.

Operating System of Computers Used to Answer Survey QuestionnaireOperating System # Resps % Resps

Windows XP 327 60.0%Macintosh 157 28.8%Windows NT 5.0 25 4.6%Windows Vista 23 4.2%Windows 98 6 1.1%Mac_PowerPC 4 0.7%Windows NT 5.2 2 0.4%Linux i686 1 0.2%

Total # Resps 545

The majority of respondents are working on a PC although a total of 29.5%responded on a computer with a Macintosh operating system.

Turning our attention to the browser, Microsoft’s Internet Explorer is stillthe most common, used by 301 of these 545 respondents, equivalent to55.2%. Approximately half as many respondents (26.8%) use a version ofFirefox while Safari came in a distant third, utilized by 15.0% of theseresearchers to access the survey questionnaire. More detailed information,including versions, are presented in the following table.

Browser Used to Answer Survey QuestionnaireBrowser # Resps # Resps

MSIE 6.0 169 31.0%MSIE 7.0 128 23.5%Firefox 2.0.0.11 126 23.1%Safari 523.12 23 4.2%Safari 419.3 20 3.7%Safari 523.12.2 18 3.3%Safari 312.6 12 2.2%Safari 523.10 7 1.3%


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Browser # Resps # RespsCamino 1.5.1 3 0.6%Firefox 2.0.0.10 3 0.6%Firefox 2.0.0.9 3 0.6%MSIE 5.23 3 0.6%DLM 4.0_1.0.0.1 2 0.4%Firefox 1.5.0.12 2 0.4%Firefox 2.0 2 0.4%Firefox 2.0.0.1 2 0.4%Firefox 2.0.0.4 2 0.4%Firefox 2.0.0.5 2 0.4%Firefox 2.0.0.7 2 0.4%Netscape 7.1 2 0.4%Camino 1.0.2 1 0.2%Camino 1.5.3 1 0.2%Firefox 1.5.0.3 1 0.2%Firefox 2.0.0.8 1 0.2%Mozilla 20050319 1 0.2%Mozilla 20060414 1 0.2%MSIE 5.22 1 0.2%Navigator 9.0b1 1 0.2%Netscape 5.0 1 0.2%Netscape 8.1 1 0.2%Opera 9.24 1 0.2%Safari 125.12 1 0.2%Safari 523.10.6 1 0.2%SeaMonkey 1.1.7 1 0.2%

Total # Resps 545


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QUESTION 91. Question:How would you best describe your organization? (Select one): Academia,Biotech/pharma industry, Hospital/medical school, Other industry,Government agency, or Private research foundation.

Rationale:With the responses to this question, we examine the distribution of theseresearchers across the six organization classifications. This will identify whereour respondents are located and the primary sources of funding for theirprotein expression work. We may also use this information in conjunctionwith responses to subsequent questions, allowing us to highlight similaritiesand differences in respondents’ usage for different organizational segments.

Results:Before analyzing, the data required some editing in order for responses to beconsistent. In order to reflect the source of funding, those working in either ahospital, medical school or health science center have all been categorized as ahospital or medical school. Researchers working in private researchfoundations, many of which have an email ending in .org, and those receivingprivate funding from organizations such as HHMI, have been classified asprivate research foundations. NIH, VA Medical Centers and militaryorganizations are considered to be government agencies.

Since this question appears towards the end of the survey questionnaire, thefollowing pie chart represents the distribution of the 405 respondents whocompleted the survey.

Academia has the largest presence, including just over 45% of these proteinexpression system users followed, at a distance by the near 30% working in ahospital or medical school laboratory. An additional 13.4% are located in theindustrial sector. The vast majority of these companies are part of thebiotechnology or pharmaceutical industry. The remaining 13.0% ofrespondents are located in a government agency or private researchfoundation.


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Analysis:On the following pages, we present a list of the organizations represented bythe respondents to this survey. These are first sorted according to the type oforganization and then presented in alphabetical order. We begin with thelocations of North American respondents involved with protein expressionand purification from the largest sector, academia.

Location of Researchers Using Protein Expression Systems, by Type of OrganizationAcademia

Atlantic Florida University Auburn University Azusa Pacific University Beckman Research Institute@City of Hope Boston University California State University, Northridge Caltech Cancer Research Center of Hawaii Clemson University Colorado State University Columbia University Cornell University Cornell University, The Boyce Thompson Institute Dalhousie University (CANADA) Drexel University Duke University D'Youville College Emory University


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Florida Institute of Technology Harvard University Indiana University-Purdue University Indianapolis Institut de Recherches Cliniques de Montréal (IRCM) (CANADA) Iowa State University Johns Hopkins University Lebanon Valley College Max-Planck-Institute for Ornithology McGill University (CANADA) Memorial University of Newfoundland (CANADA) Michigan State University Montana State University North Carolina State University Northeastern University (NEU), Center for Drug Discovery NYU Institute of Environmental Medicine, Tuxedo Oakland University School of Health Sciences Ohio State University Oklahoma State University Oregon State University Pennington Biomedical Research Center Princeton University Purdue University Rockefeller University Rush University Rutgers University Saint Louis University Saint Mary's University of Minnesota Southern Illinois University Stanford University State University of New York at Buffalo Stony Brook University Temple University Texas A&M University Thomas Jefferson University Thomas Jefferson University, Kimmel Cancer Center Tufts University Tulane University Union University Université de Montréal (CANADA) University at Buffalo University at Buffalo University of Alabama at Birmingham University of Alabama, MINT University of Arizona University of Arizona, Tucson University of Calgary (CANADA) University of California, Berkeley University of California, Davis University of California, Los Angeles University of Chicago


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University of Cincinnati University of Colorado Health Sciences University of Colorado, Boulder Coop Inst for Research in Environmental Scis

(CIRES) University of Colorado, Colorado Springs University of Connecticut University of Delaware University of Denver University of Florida University of Georgia University of Georgia College of Veterinary Medicine University of Guelph (CANADA) University of Houston University of Illinois at Chicago University of Illinois at Urbana University of Illinois, Urbana University of Iowa University of Kansas University of Kentucky College of Dentistry University of Louisiana at Lafayette University of Louisville University of Maryland Biotechnology Institute University of Maryland, School of Pharmacy University of Massachusetts University of Michigan University of Minnesota University of Missouri, Columbia University of Missouri, Kansas City University of North Carolina, Chapel Hill University of Pennsylvania University of Pennsylvania Institute of Medicine and Engineering University of Pittsburgh University of Pittsburgh Graduate School of Public Health University of Southern California University of Tennessee, Knoxville University of Texas Southwestern, Dallas University of Virginia University of Washington University of Wisconsin Madison University of Wisconsin Madison, Waisman Center Virginia Commonwealth University Virginia Polytechnic Institute and State University Virginia Tech Washington State University Washington University in Saint Louis Wayne State University Youngstown State University

Hospital/Medical School Beth Israel Deaconess Medical Center


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Boston University Medical Center Boston University School of Medicine Boys Town National Research Hospital Brigham and Women's Hospital Center for the Health Sciences David Geffen School of Medicine at UCLA Columbia University Cornell Medical School Creighton University Dana-Farber Cancer Institute Dartmouth Medical School David Geffen School of Medicine @UCLA Duke University Medical Center Emory University School of Medicine Harvard Medical School Indiana University School of Medicine, Indianapolis Indiana University, Bloomington Indiana University-Purdue University Indianapolis International Center of Public Health Johns Hopkins Medical Institutions Johns Hopkins School of Public Health Juraviski Cancer Centre (CANADA) LSU Neuroscience Center Massachusetts General Hospital Medical College of Wisconsin Nationwide Children's Hospital Research Institute North Shore Long Island Jewish Health System NYU School of Medicine, New York Oregon Health Sciences University Penn State University College of Medicine Stony Brook Medical Center SUNY Downstate Medical Center Thomas Jefferson University University of Alabama at Birmingham Medical School University of Arizona University of California, Davis University of California, San Diego School of Medicine University of California, San Francisco School of Medicine University of Chicago University of Cincinnati University of Colorado Health Sciences Center at Fitzsimons University of Colorado Health Sciences Center, Aurora University of Kentucky College of Medicine University of Louisville School of Medicine University of Maryland University of Maryland School of Medicine University of Michigan University of Minnesota University of Mississippi Medical Center University of Nebraska Medical Center University of New Mexico School of Medicine


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University of North Carolina School of Medicine, Chapel Hill University of North Texas Health Science Center University of Pennsylvania, Ryan Veterinary Hospital University of Pittsburgh School of Medicine University of Rochester Medical Center University of South Carolina School of Medicine University of South Florida University of Southern California University of Texas Health Center @ Tyler University of Texas Health Sciences Center, San Antonio University of Texas Medical Branch University of Texas Southwestern Medical Center at Dallas University of Texas, Houston University of Utah Health Sciences Center University of Virginia University of Washington, Seattle Vanderbilt University Wake Forest University School of Medicine Washington University School of Medicine in Saint Louis Wayne State University School of Medicine Winthrop University Hospital Yale University School of Medicine

Biotechnology/Pharmaceutical Industry Adnexus Therapeutics Amgen BioMarin Pharmaceutical Bio-Rad Laboratories Biosource Cell Signaling Technology Colgate Palmolive EDVOTEK Eli Lilly & Company EMD-Merck EnVivo Pharmaceuticals Epicentre Genentech Gen-Probe GenVec, Inc Incyte Corporation Intermune Lancaster Laboratories Lipid Sciences, Inc Merck & Co Inc Millennium Pharmaceuticals Monsanto Neose Technologies, Inc Olympic Biotechology Otsuka Pharmaceuticals Perkin Elmer


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Pfizer Global Research & Development Precision Incorporated Promega Protea Biosciences Proteon Therapeutics Roche Molecular Biochemicals Sangamo BioSciences, Inc. Sanofi-Aventis Schering-Plough Sigma-Aldrich Inc TetraLogic Pharmaceuticals Thermo Fisher Ventana Medical Systems VLP Biotech Wyeth Pharmaceuticals

Government Agency Argonne National Lab Bay Pines VA Healthcare System (BPVAHCS) Brookhaven National Laboratory CDC/Nat'l Institute for Occupational Safety & Health (NIOSH) Toxicology and

Molecular Biology Branch (TMBB) Idaho National Laboratory LA County Department of Health Services (DHS) Lawrence Livermore National Laboratory National Animal Disease Center NIH/Nat’l Cancer Institute (NCI), Center for Cancer Research (CCR), Shrewsbury NIH/Nat’l Cancer Institute (NCI), Frederick NIH/Nat’l Cancer Institute (NCI), SAIC-Frederick NIH/Nat’l Institute of Allergy and Infectious Diseases (NIAID) NIH/Nat’l Institute of Environmental Health Sciences (NIEHS) NIH/Nat’l Institute of Neurological Disorders and Stroke (NINDS) NIH/Nat’l Institute on Aging (NIA) NIH/Nat’l Institute on Alcohol Abuse and Alcoholism (NIAAA) Oregon National Primate Research Center Uniformed Services University of the Health Sciences (USUHS) US Army Medical Research Institute of Infectious Diseases (USAMRIID) US Environmental Protection Agency (USEPA) US Naval Research Laboratory USDA-ARA Southern Regional Research Center VA Medical Center, Long Beach VA Medical Center, Memphis VA Medical Center/Harvard Medical Center VA Medical Center/Wayne State University Walter Reed Army Institute of Research (WRAIR)

Private Research Foundation Aeras Global TB Vaccine Foundation Cedars Sinai Medical Center Cleveland Clinic Foundation


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Doheny Eye Institute Donald Danforth Plant Science Center HHMI, Janelia Farm Molecular Biology Lovelace Respiratory Research Institute Mayo Clinic (Cancer Center, Jacksonville) Mayo Clinic Pharmacology and Cancer Center, Scottsdale Mayo Clinic, Rochester Mayo Foundation MD Anderson Cancer Center, Houston Memorial Sloan Kettering Cancer Center (MSKCC) Molecular Medicine Research Institute (MMRI) Roswell Park Cancer Institute St. Jude Children's Research Hospital The Scripps Research Institute (TSRI) Van Andel Research Institute

Other Industry Charles River Laboratories DuPont Hitachi Chemical Research Center Kinetic Concepts Inc. (KCI) Midwest Research Institute Nutreco Canada Agresearch (CANADA) TJ Technologies


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QUESTION 92. Question:What most closely fits your job description?: Laboratory technician/researchassistant, laboratory manager/director/supervisor, research associate, graduatestudent, postdoctoral fellow, laboratory scientist, principal investigator,project manager, senior scientist, department head, vice president, corefacility director, purchasing agent/buyer, scientific writer or journalist, salesor marketing specialist.

Rationale: This question provides a description of our respondent’s position in the lab.We would hope for a good cross-section of respondents, to obtain feedbackfrom those working at the bench (such as laboratory technicians andassistants, postdocs and graduate students), as well as the principalinvestigators, laboratory managers, and senior scientists who in general, havegreater control over purchasing decisions.

Results:The following horizontal bar graph depicts the distribution of the 405researchers working with protein expression or purification who completedthis questionnaire.


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Two of the fifteen job descriptions itemized on this survey (purchasingagent/buyer and scientific writer or journalist) are not represented in this poolof respondents. In fact, these two options, along with sales or marketingspecialist, were included here so that we could identify respondents which wemay decide not to include in the respondent base. At this time, we willinclude all respondents in the analysis. However, we will watch the responsesfrom these specialists (from PerkinElmer and Sigma-Aldrich) carefully tomake sure that they are not biasing the data.

Looking at the distribution shown on the previous horizontal bar graph,principal investigators are very well represented, accounting for fully 41% ofour respondents. Considering the high percentage from the academic sectorand hospital/medical school sectors, this is perhaps not surprising. Laboratorymanagers, directors or supervisors make up the second largest group based onjob description followed by nearly equal shares (of just under 10%) forpostdoctoral fellows, senior scientists and laboratory scientists. Researchassociates are the only remaining group accounting for at least 5% of therespondent pool.

Analysis: Despite the heavy concentration of principal investigators, we do haveresearchers representing all levels. Adding the percentage of laboratorymanagers and senior scientists to the share of PIs, we conclude that 62.5% ofthe 405 respondents currently involved with protein expression work areconsidered to be upper level researchers. Adding the few respondentsdescribing themselves as a core facility director, vice president or departmenthead increases this to 65.9% share. The remaining respondents are more likely to be working at the bench. Theseinclude a further 8.1% of lower level scientists, consisting of graduatestudents, lab technicians and research assistants. The remaining 26.0% areconsidered to be mid-level scientists, and consist of near equal number ofpostdoctoral fellows and laboratory scientists, research associates and a smallnumber of project managers.

In conclusion, we believe that we have obtained an excellent cross-section ofprofessional positions with plenty of upper-level qualified respondents and asufficient number of those working at the bench.


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QUESTION 93. Question:How many years of experience do you have with protein expression systems?: ________ years

Rationale:This question was designed to measure the respondents’ level of experiencewith these systems. Ideally, we would prefer to see a broad spectrum ofresponses varying from relative ‘beginners’ to highly experienced respondents.We will examine the level of experience for all respondents and check for anysignificant differences between researchers from different types oforganizations.

Results:The 405 researchers currently utilizing protein expression systems whocompleted the survey questionnaire, and therefore, answered this question,report a combined total of 4,550 years of experience. Despite the wide rangeof individual responses, varying from 1 to a maximum of 37 years ofexperience, the 11.2 arithmetic mean is very similar to the 10.0 year medianand identical mode level of experience with protein expression systems.

The distribution of responses is shown in the following vertical bar graph.


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This data forms a bell-shaped curve centered on the 30.6%, and highestconcentration of researchers, reporting from 6 to 10 years of experience withprotein expression systems. Adding the near 25% of respondents with over10 but no more than 15 years working in this field includes just over half,54.3%, of the pool of respondents completing this survey. As seen here, theremaining half are split relatively evenly between those who are relatively newto this technique, with 5 years of experience or less, and researchers withextensive experience of more than 15 years working with these systems.

Analysis:Respondents to this survey have a broad range of experience, including thosejust starting in this field, as well as a considerable proportion having a wealthof experience with protein expression systems.

As shown in the following table, this is true of researchers from all six types oforganizations. Although the number of respondents varies widely, the range,mean and median years of experience are remarkably similar.

Years of Experience with Protein Expression Systems, by Type of OrganizationType of Organization # Resps Range Mean Median

Academia 186 1-30 10.6 10.0Hospital/medical school 112 2-37 12.5 12.0Biotech/pharma industry 46 1-22 10.8 11.5Government agency 33 1-25 11.9 12.0Private research foundation 20 2-20 10.7 10.0Other industry 8 1.5-20 9.7 10.0

Total 405 1-37 11.2 10.0

We expect that this will enable them to provide a variety of perspectives andvaluable insight regarding their experiences in this area, and are undoubtedlywell qualified to respond to the questions on this survey.


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QUESTION 94. Question:Please indicate below your primary scientific discipline to the one in whichyou are involved (Select one): Biochemistry, biotechnology, cell biology,endocrinology, genetics, genomics, microbiology, molecular biology,neuroscience, pharmacology, pathology or other.

Rationale: With the responses to this question, we will examine the primary scientificdiscipline of respondents who are currently working with protein expressionsystems. Results: The results for the 405 respondents who answered this question are presentedin the following horizontal bar chart.

Analysis: Molecular biology is the most common scientific discipline, mentioned bynearly 28% of the respondents to this survey. Accounting for near 23% ofrespondents, biochemistry is the second most prevalent discipline, followedby the 18% defining themselves as cell biologists. Microbiology andneuroscience are a distant fourth and fifth place, each accounting forapproximately 7% of researchers. Biotechnology is the only remaining


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itemized discipline represented by at least 5% share. In fact, the remainingfive options (genetics, pharmacology, endocrinology, genomics, andpathology) combined make up a further 5.5% of our respondent pool withthe final near 6% consisting of respondents involved in an ‘other’ unlisteddiscipline. It is interesting to note that this distribution is relatively similar to thosereported by respondents to the 2003 MSPPSA protein expression study withthe single exception of a decrease (by half) in the proportion of respondentsworking in biotechnology.


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QUESTION 95. Question:Do you work in a core facility that provides protein expression services?: Yes,I work in a core facility that provides these services; I work in a core facilitywhich does not provide protein expression services; No, I don’t work in acore facility.

Rationale:Core facilities tend to have a unique set of requirements, sample throughput,priorities and needs, particularly if they are performing protein expression forother labs as a service. This question was designed to identify thoseresearchers within our respondent pool. Later, we may examine the responsesto other questions for respondents in core facilities separately from thoseworking in a traditional laboratory.

Results:As shown in the following pie chart, the vast majority of these 405respondents do not work in a core laboratory. Of the 6.26% (equivalent to29 researchers) located in one of these central facilities, nearly half of these donot provide protein expression services to other laboratories.


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QUESTION 3. Question:You can answer the following questions based upon your own personal use ofrecombinant protein expression or based upon the combined usage for yourentire laboratory.Will you be answering questions based upon your individual usage or basedupon the combined usage of your laboratory?: individual or laboratory.

Rationale:The responses to this question indicate the basis of the responses. It will beparticularly important to take this factor into account when evaluating theannual budget for recombinant protein expression.

Results:As shown in the following pie chart, just over two out of every threerespondents will be answering this survey on behalf of their laboratory.

Analysis:Consistent with previous surveys covering other areas of the life scienceresearch market, the majority of these researchers are more comfortableresponding on behalf of their laboratory rather than for their personal usage.Considering the large proportion of upper-level scientists answering thisquestionnaire, this is perhaps to be expected.


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QUESTION 4. Question:You indicated that you will be describing protein expression usage basedupon the combined usage of your laboratory. Please let us know how manyresearchers in your laboratory are currently involved with protein expressionand subsequent purification and are covered by your laboratory's budget.:______ researchers currently involved with protein expression/purificationand covered by the lab’s budget

Rationale:Respondents answering on behalf of their laboratories were directed to thissupplemental question asking for the number of lab researchers who areinvolved with protein expression and covered by the lab budget. Inconjunction with subsequent questions regarding laboratory throughput andspend, for example, laboratory values will be divided by this factor to obtainan estimate of usage on an individual basis. This permits the directcomparison of these values with the responses describing individual usage.

Results:The number of lab researchers currently involved with protein expression andsubsequent purification who are also covered by the laboratory budget of 359respondents to this survey are presented in the following vertical bar graph.


-44-

Although these respondents report values ranging from 2 to 50 researchers,fully 65.9% are describing protein expression and associated purificationperformed 2 to 4 researchers in their laboratories, with 40% answering forlabs of 3 or 4 researchers working in this area. Not surprisingly, the statisticalmedian and mode is equal to 3.0 researchers involved with the expression orassociated purification of proteins while the mean value is slightly higher,calculated to be 4.7 researchers per lab. These respondents represent thecombined work of 1,688 North American bioresearchers.

Analysis:Next, we examined the number of researchers per lab involved with proteinexpression for respondents who completed the survey and therefore indicatedwhether they work in a core facility. The results are presented in thefollowing table. Note that the mean for the 268 respondents completing thesurvey is slightly (but not significantly) lower than that for all 359 researchersanswering this question.

Statistical Number of Researchers/Laboratory Involved with Protein Expression &Purification, by Type of Laboratory

Type of Lab #Resps

Mean Median Mode

Non-core lab 247 4.3 3 3Core/provides protein expression services 12 11.8 6 3Core/no services 9 4.2 4 -

All respondents 268 4.6 3 3

As might be expected, we see that core labs providing protein expressionservices are significantly larger than either non-core labs or core facilities notproviding these services.

Finally, as mentioned above, the 359 respondents answering this survey basedon the protein expression and subsequent purification work performed bytheir entire lab, describe the output of a total of 1,688 North Americanresearchers. Adding the 186 respondents answering on an individual basis, weconclude that this data represents the protein expression work of a combinedtotal of 1,874 North American researchers.


-349-

XV. THEQUESTIONNAIRE


-350-

2007 Protein Expression & Purification Systems Survey

To begin, please enter the UserID and password from your survey invitation here:

User ID

Password

Next

© 2007 PhorTech International

Start


Thank you for taking time to answer our survey questionnaire. This survey is for researchers currently using protein expression systems and subsequent protein purification systems in their work. We estimate that completing this survey will take you 12 minutes or less.

We will be pleased to send your choice of a nice selection of free gifts as a thank you for taking part in the survey. You can choose between a new limited edition tee shirt with the message “When it comes to protein expression, my opinion counts” (in M, L or XL). The specially commissioned graphic is shown at left.

You can also select a gift card good for a full pound of Starbucks coffee (House Blend), our quality laser pointer (a great gift item), an Inova brilliant LED keychain microlight, a stainless steel executive pocket

knife, a crisp new 5 Euro banknote, a $5 gift certificate good for on-line purchases at Amazon.com, or a $5 gift card to Barnes & Noble, good towards a book, CD, or cup of coffee on us.

Alternatively, we are also offering the option to donate $5 in your name to Habitat for Humanity instead of receiving a personal gift.

Please be sure to select your choice of free gift at the end of the survey. Thank you for participating.

Do you currently use any recombinant protein expression systems in your work?

nmlkj Yes, we currently use recombinant protein expression systems

nmlkj No, we do not use recombinant protein expression systems.

You can answer the following questions based upon your own personal use of recombinant protein expression or based upon the combined usage for your entire laboratory.

Will you be answering questions based upon your individual usage or based upon the combined usage for your laboratory?

nmlkj individual nmlkj laboratory

Next

in t ro

Q 1

Q 3

0% 100%



You indicated that you will be describing protein expression usage based upon the combined usage of your laboratory.

Please let us know how many researchers in your laboratory are currentlyinvolved with protein expression and subsequent purification and are covered by your laboratory's budget.

researchers currently involved with protein expression/purif icat ion and covered by the lab's budget

Next

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Q 4


Which of the following cell systems are currently being used for protein expression? (Please check ALL that apply).

gfedc cell-free

gfedc prokaryotic

gfedc yeast

gfedc insect

gfedc plant

gfedc mammalian

gfedc other:

What are the main reasons you use the expression systems that you have chosen? (Please explain in detail in the space below).

Next

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Q 2

Q2_1

Q2_2

Q2_3

Q2_4

Q2_5

Q2_6

Q2_7 Q2_7_other

Q 2 a


Considering your usage, how much do you spend on recombinant protein expression products in a typical year? Please include expression kits and vectors plus associated nucleic acid purif ication, host strains, and cel l culture media in your totals. (Please specify both the amount and the currency.)

per year on average in Select currency:

What percent change do you foresee in your use of protein expression systems over the coming 12 months? (Please enter an estimate and indicate if positive or negative.)

% Increase Decrease No change nmlkj nmlkj nmlkj

And, considering your usage, how much do you spend on associated protein purif icat ion products in a typical year? Please include downstream lysis, columns, instrumentation, and other purif ication products in your totals. (Please specify both amount in the currency you indicated above.)

per year on average for puri f icat ion of these expressed proteins

And, what percent change do you foresee in your use of protein purif icat ion for these expressed proteins over the coming 12 months? (Please enter an estimate and indicate if positive or negative.)

% Increase Decrease No change nmlkj nmlkj nmlkj

Next

0% 100%


Q 5

[SCR IPT ]

Q5_ecurrency

Q 6

Q 5 a

[SCR IPT ]

Q 6 a


For every system you use, please identify each supplier, and indicate the percent of yourtotal expression budget you spend with that supplier for that cell system. (Please begin with your major suppliers and spends).

Sys tem Supp l i e r % To ta l Exp ress i on

Budge t

a. Select System:

b. Select System:

c. Select System:

d. Select System:

Why did you choose these suppliers for your expression products? (Please be as specific as possible and be sure we can tie the comment to a supplier).

Next

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Q 7

Q7_r1_c1 Q7_r1_c2 Q7_r1_c3

Q7_r2_c1 Q7_r2_c2 Q7_r2_c3

Q7_r3_c1 Q7_r3_c2 Q7_r3_c3

Q7_r4_c1 Q7_r4_c2 Q7_r4_c3

Q 8


For every purification product class you use, please identify each supplier, and indicate the percent of your total expressed protein purification budget you spend with that supplier for that product class. (Please focus on your major suppliers and spends).

Supp l i e r % Tota l Pur i f i ca t i on

Budge t

Columns

Lysis system

Instrumentation

Why did you choose these suppliers for the purification of your expressed proteins (Please be as specific as possible and be sure we can tie the comment to a supplier).

Next

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Q 7 a

Q7a_r3_c1 Q7a_r3_c2

Q7a_r1_c1 Q7a_r1_c2

Q7a_r2_c1 Q7a_r2_c2

Q 8 a


Are there suppl iers of protein expression systems or expressed protein purif ication systems from whom you wouldn't buy?

Yes, the fol lowing:

No

nmlkj

nmlkj

If yes, please explain because:

Next

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Q 1 0


Please list the improvements you would like to see in specific protein expression products?

Please list the improvements you would like to see in products for the purification ofexpressed proteins?

Next

0% 100%


Q 1 1

Q 1 1 a


From the alphabetic list of expression/purification product suppliers below, please indicate the suppliers you recognize. For example, you use their products on a regular basis or are familiar with their offerings. (Please select ALL that apply. You may identify one additional company of your choice).

gfedc Abnova gfedc GE Healthcare gfedc Sigma

gfedc Active Motif gfedc GeneCopoeia gfedc Stratagene

gfedc Agilent

gfedc

iNtRON Biotechnology

gfedc Takara Bio/Clontech

gfedc

Applied Biosystems/Ambion

gfedc Invitrogen

gfedc Thermo Fisher Scientific

gfedc Bio-Rad Laborator ies

gfedc

New England Biolabs

gfedc Wako Pure Chemicals

gfedc

BD Biosciences/Pharmingen

gfedc PerkinElmer

gfedc Waters

gfedc CellFree Sciences

gfedc Promega

gfedc

Other

gfedc Cosmo Sciences gfedc Qiagen

gfedc EMD/Novagen gfedc Roche

From the following list, please rate the importance of each of the following factors in the decision to select a protein expression system or purification system supplier. (Using a 10 point scale, where '1' means very important and a '10' means not at all important. You may use a rating value more than once).

Very

impor tan t 1 2 3 4 5 6 7 8 9

Not a t a l l impor tan t

10

Procedures to minimize hands-

on time nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Reliable performance nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Previous experience nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Reputation of suppl ier nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Availabil ity/ease of ordering nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Col league's recommendation nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Literature references nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Value for money nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Consistent quality nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Ease o f use nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj nmlkj

Next

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Q 1 2

Q12_1 Q12_10 Q12_19

Q12_2 Q12_11 Q12_20

Q12_3 Q12_12 Q12_21

Q12_4 Q12_13 Q12_22

Q12_5 Q12_14 Q12_23

Q12_6 Q12_15 Q12_24

Q12_7 Q12_16 Q12_25 Q12_25_other

Q12_8 Q12_17

Q12_9 Q12_18

Q 1 3

Q13_r2 Q13_r2 Q13_r2 Q13_r2 Q13_r2 Q13_r2 Q13_r2 Q13_r2 Q13_r2 Q13_r2











From the alphabetic pull-down lists of protein expression and purification suppliers, please mark the one you would rank highest in each of thefollowing areas you considered important. (You may choose a supplier more than once).

H ighes t Rank i ng Supp l i e r

Value for money

Procedures to minimize hands-on time

L iterature references

Col league's recommendation

Previous experience

Ease o f use

Availabil ity/ease of ordering

Reliable performance

Consistent qual i ty

Reputation of suppl ier

Next

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Q 1 4

Q14_r1_c1

Q14_r2_c1

Q14_r3_c1

Q14_r4_c1

Q14_r5_c1

Q14_r6_c1

Q14_r7_c1

Q14_r8_c1

Q14_r9_c1

Q14_r10_c1


The next series of questions deals with the proteins you are expressing and their subsequent purification.

What is the origin of the proteins you are expressing? (Please check ALL that apply).

gfedchuman

gfedcplant

gfedc yeast

gfedc mammal

gfedcviral

gfedc

other animal

gfedcprokaryotic

gfedc

other:

What types of proteins are you expressing? (Please check ALL that apply).

gfedc

other secreted

gfedcnuclear

gfedc membrane

gfedccytoplasmic

gfedcantibody

gfedc

other:

What characteristics does your expressed protein need to have? (Please check ALL that apply).

gfedc soluble protein

gfedc functional protein

gfedc correct folding

gfedc bonaf ide PTMs

gfedc other:

What post-translational modifications does your expressed protein need to have? (Please check ALL that apply).

gfedc glycosylation-N-l inkage

gfedc glycosylation-O-l inkage

gfedc acylation

gfedc acetylation

gfedc phosphorylat ion

gfedc other:

Next

0% 100%

Q 2 0

Q20_1 Q20_6 Q20_4 Q20_3

Q20_7 Q20_5 Q20_2 Q20_8 Q20_8_other

Q 2 1

Q21_2 Q21_5 Q21_4

Q21_3 Q21_1 Q21_6 Q21_6_other

Q 2 9

Q29_1

Q29_2

Q29_3

Q29_4

Q29_5 Q29_5_other

Q 3 0

Q30_1

Q30_2

Q30_3

Q30_4

Q30_5

Q30_6 Q30_6_other


How do you purify the proteins you express? (Please check ALL that apply).

gfedc gel f i ltration

gfedc

ion exchange

gfedc

salt or organic fractionation

gfedc

other affinity chromatography

gfedc

metal chelating resin

gfedc

other:

How many chromatography steps do you typically perform to get your protein of interest purified to your satisfaction?

chromatography purif ication steps typical ly

Next

0% 100%


Q 2 3

Q23_1 Q23_3 Q23_5

Q23_2 Q23_4 Q23_6 Q23_6_other

Q 2 4


For each of the expression systems you use most frequently, please indicate the yield you typically obtain (in terms of milligrams of protein). Also, please indicate how much expressed protein (in milligrams) you typicaly require.

Expression System Used Yield (mg protein) Protein Quantity

Required (mg)

a. Select expression system:

b. Select expression system:

c. Select expression system:

How many proteins or variants do you express in a month?

per month

Next

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Q 2 5

Q25_r1_c1 Q25_r1_c2 Q25_r1_c3

Q25_r2_c1 Q25_r2_c2 Q25_r2_c3

Q25_r3_c1 Q25_r3_c2 Q25_r3_c3

Q 2 6


0% 100%


f i n

Note:

T h i s p age ha s a l i n k on i t . When the su rvey

i s run th i s page w i l l be red i rec ted to :

http://www.phortech.com/pex2/cgi-

bin/ciwweb.pl?

studyname=pex2&UserName=

&Password= &IvL=

&cf= &pro= &yst=

&ins= &mam=

&hid_test_mode=1

[SCRIPT]

[SCRIPT] [SCRIPT]

[SCRIPT] [SCRIPT]

[SCRIPT] [SCRIPT]

[SCRIPT]


Sorry, but you must be currently involved with protein expression research to participate in this survey. Please stop now. We hope to invite you to a more appropriate survey in the future.

Best regards,

The PhorTech Team

0% 100%


ou t


WARNING - From this stage on in the survey, DO NOT USE your browser's BACK BUTTON. If you do, you may not be able to return to

this point or complete the survey to claim your free gift.

To begin, please enter the UserID and password from your survey invitation here:

User ID

Password

Next


Start




Do you use an automated protein purification system?

gfedc

Yes, I use an automated protein purif icat ion system for larger-scale preps

gfedc

Yes, I use an automated protein purif ication system for small samples in a high throughput format

gfedc

No, but I plan to add this capabi l i ty within the next 12 months

gfedc

No, and I do not plan to add this capabi l i ty within the next 12 months

Next

0% 100%


Q 2 7

Q27_1

Q27_2

Q27_3

Q27_4


WARNING - From this stage on in the survey, DO NOT USE your browser's BACK BUTTON. If you do, you may not be able to return to this point or

complete the survey to claim your free gift.

You indicated that you are currently using an automated protein purification system. Please tell us a little about your purification system.

I use this brand and model

acquired in year

For what downstream applications do you express proteins? (Please be as SPECIFIC as possible).

Next

0% 100%


Q 2 8

Q 3 1




The next questions pertain to cell-free (in-vitro) expression systems

Considering your usage, how many total cell-free (in-vitro) preps do you perform in a typical month?

cell-free (in-vitro) preps per month, on average

Why do you choose to use cell-free (in-vitro) expression systems in your work? (Please explain in detail in the space below).

Which of the following cell-free systems are currently being used in your laboratory for protein expression? (Please select ALL that apply).

gfedc Human

gfedc

Wheat germ

gfedc

Other:

gfedc Insect gfedc E. coli

gfedc

Rabbit reticulocyte

gfedcFungal/Yeast

Which of the following two procedures do you prefer to use?

nmlkj Use a s ingle-step procedure (Transcript ion coupled to translat ion in the reaction)

nmlkj Use a two-step procedure (Transcribe mRNA in a separate reaction and add it to the translation mix)

Next

0% 100%


Q 5 0

[SCR IPT ]

Q 5 1

Q 5 3

Q53_6 Q53_2 Q53_7 Q53_7_other

Q53_4 Q53_3

Q53_1 Q53_5

Q 5 3 a




Which promoter(s) do you use most often with cell-free expression? (Please select ALL that apply).

gfedcT7

gfedcT3

gfedcCMV

gfedcSP6

gfedc

Other:

Which type of template do you prefer to use for cell-free translation reactions? (Please select ALL that apply).

gfedc Plasmid DNA

gfedc PCR product

gfedc Purified mRNA

gfedc Total RNA

gfedc

A versati le vector containing multiple cloning sites, promoter, and poly A tail

Regarding your template mRNA, which do you prefer?

nmlkj Cap-dependent translat ion

nmlkj Cap-independent (IRES dependent) translat ion

nmlkj No preference

Which epitope tag(s) for purification, detection, and analysis of recombinant proteins do you use most often with cell-free systems? (Please select ALL that apply).

gfedcPolyHis

gfedcFLAG

gfedc

c-myc

gfedc Hemagglutinin (HA)

gfedcMBP

gfedcGST

gfedcV5

gfedc

Other:

Next

0% 100%


Q 5 4

Q54_2 Q54_3 Q54_4 Q54_1 Q54_5 Q54_5_other

Q 5 5

Q55_1

Q55_2

Q55_3

Q55_4

Q55_5

Q 5 6

Q 5 7

Q57_5 Q57_7 Q57_4 Q57_2

Q57_6 Q57_3 Q57_1 Q57_8 Q57_8_other




Which detection system(s) do you prefer for in vitro translated proteins? (Please select ALL that apply).

gfedc Chemiluminescence-based detect ion systems

gfedc Fluorescence-based detect ion systems

gfedc Radioactivity-based detect ion systems

gfedc Other:

gfedc No preference

Are you considering moving into a high-throughput (96 or 384 well format) cell-free expression system?

nmlkj Yes

nmlkj No

nmlkj Don't know

If so, please elaborate in the space below. (Let us know your time-frame, likely suppliers, anticipated throughput, etc.)

Next

0% 100%


Q 5 8

Q58_3

Q58_2

Q58_1

Q58_4 Q58_4_other

Q58_5

Q 5 9

Q 5 9 a


WARNING - From this stage on in the survey, DO NOT USE your browser's BACK BUTTON. If you do, you may not be able to return to this point or complete the survey to claim your free gift.

The next questions pertain to prokaryotic expression systems

Considering your usage, how many total prokaryotic preps do you perform in a typical month?

prokaryotic preps per month, on average

What prokaryotic expression vector(s) are you using? (Multiple answers may be chosen). Please add any additional vectors under 'other'. If more than two, please list all separated by commas.

gfedcThioFusion

gfedcProEX

gfedcPinPoint

gfedc pBAD

gfedc

Other:

gfedc pFLAG

gfedcpEcoli

gfedc pT7

gfedc Xpress

gfedc

Other:

gfedc pET

gfedcFlexi

gfedcpGST

gfedcQIAExpress

What promoter(s) do you use most often? (Multiple answers may be chosen). Please add any additional promoters under 'other'. If more than two, please list all separated by commas.

gfedcaraB

gfedclac

gfedc T7

gfedc

Other:

gfedctac

gfedcSP6

gfedc T3

gfedc

Other:

gfedcT5

gfedctrc

gfedc

lambda p1

What fusion tags do you use for purification or detection of recombinant proteins in prokaryotic cells? (Multiple answers may be chosen). Please add any additional fusion tags under 'other'. If more than two, please list all separated by commas.

gfedc

His-tag/polyhistidine

gfedc S-tag

gfedc acTEV

gfedc Strep-tag gfedc rTEV gfedc FLAG

gfedc c-myc

gfedc T7-tag

gfedc

Other:

gfedc thioredoxin

gfedc

maltose binding protein

gfedc

Other:

gfedc GST gfedc Xpress

What protease cleavage enzymes do you use most frequently? (Multiple answers may be chosen).

gfedc factor Xa

gfedc

PreScission Protease

gfedc rTEV

gfedc

enterokinase (catalytic subunit)

gfedc TAGzyme

gfedc

other:

gfedc thrombin

gfedc

enterokinase (holoenzymes)

gfedc do not use these enzymes

Next

0% 100%

Q 8 0

[SCR IPT ]

Q 8 1

Q81_5 Q81_4 Q81_7 Q81_3 Q81_13 Q81_13_other

Q81_1 Q81_12 Q81_10 Q81_6 Q81_14 Q81_14_other

Q81_2 Q81_11 Q81_8 Q81_9

Q 8 2

Q82_2 Q82_1 Q82_7 Q82_10 Q82_10_other

Q82_6 Q82_9 Q82_8 Q82_11 Q82_11_other

Q82_3 Q82_5 Q82_4

Q 8 3

Q83_7 Q83_3 Q83_12

Q83_8 Q83_11 Q83_1

Q83_4 Q83_6 Q83_13 Q83_13_other

Q83_5 Q83_10 Q83_14 Q83_14_other

Q83_2 Q83_9

Q 8 4

Q84_6 Q84_2 Q84_5

Q84_4 Q84_7 Q84_8 Q84_8_other

Q84_3 Q84_1 Q84_9




The next questions pertain to yeast expression systems

Considering your usage, how many total yeast preps do you perform in a typical month?

yeast preps per month, on average

What yeast strains do you use to produce recombinant proteins? (Multiple answers may be chosen).

gfedc Schizosaccharomyces pombe

gfedc Saccharomyces cerevisiae

gfedc Pichia pastoris

gfedc Other:

What fusion tags do you use for purification of recombinant proteins in yeast cells? (Multiple answers may be chosen). Please add any additional fusion tags under 'other'. If more than two, please list all separated by commas.

gfedc


gfedcrTEV

gfedc S-tag

gfedc thioredoxin

gfedc

c-myc

gfedc GST

gfedc T7-tag

gfedcFLAG

gfedc

Other:

gfedc Strep-tag

gfedcXpress

gfedc

Other:

gfedc


gfedcacTEV

Next

0% 100%


Q 7 0

[SCR IPT ]

Q 7 1

Q71_2

Q71_1

Q71_3

Q71_4 Q71_4_other

Q 7 2

Q72_7 Q72_11 Q72_3

Q72_5 Q72_4 Q72_2

Q72_6 Q72_1 Q72_13 Q72_13_other

Q72_8 Q72_9 Q72_14 Q72_14_other

Q72_10 Q72_12




The next questions pertain to insect expression systems

Considering your usage, how many total insect preps do you perform in a typical month?

insect preps per month, on average

Do you use baculovirus to produce recombinant proteins in insect cells or direct transformation of insect cells?

gfedc yes, I use baculovirus.

gfedc yes, I use direct transformation of insect cel ls.

gfedc no, I do not use insect cel ls.

Next

0% 100%


Q 6 0

[SCR IPT ]

Q 6 1

Q61_1

Q61_2

Q61_3




What types of baculovirus DNA do you use to generate recombinant virus? (Multiple answers may be chosen).

gfedc

BaculoGold (Pharmingen)

gfedc BaculoDirect (Invitrogen)

gfedc

BacVector 1000 etc. (Novagen)

gfedc BakPak (Clontech)

gfedc

Bac-to-Bac (Invitrogen)

gfedc

Other:

gfedc

Bac-N-Blue (Invitrogen)

What baculovirus transfer vectors do you use most often? (Multiple answers may be chosen).

gfedcpBlueBAcHis2

gfedcpFastBAc

gfedc pBlueBac 4.5

gfedc pMelBac

gfedc pTriEx

gfedc

Other:

gfedc

pVL1392 or pVL1393

gfedcpBacPAK

gfedc pBAC

gfedc

pQE-TriSystem

Next

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Q 6 2

Q62_5 Q62_6

Q62_4 Q62_1

Q62_3 Q62_7 Q62_7_other

Q62_2

Q 6 3

Q63_2 Q63_4 Q63_6

Q63_8 Q63_3 Q63_10 Q63_10_other

Q63_5 Q63_1

Q63_7 Q63_9




Do you express recombinant proteins in insect cells using one of these nonlytic stable systems? (Multiple answers may be chosen).

gfedc DES - Drosophila Expression System (Invitrogen)

gfedc pIE System (Novagen)

gfedc Other:

What insect lines do you use to produce recombinant proteins in insect cells? (Multiple answers may be given).

gfedc Spodoptera Sf21 cel ls

gfedc Spodoptera Sf9 cel ls

gfedc Drosophila S2 cel ls

gfedc Trichoplusia High Five cells

gfedc Other:

What fusion tags do you use for purification of recombinant proteins in insect cells? (Multiple answers may be chosen). Please add any additional fusion tags under 'other'. If more than two, please list all separated by commas.

gfedc FLAG gfedc T7-tag gfedc S-tag

gfedc c-myc gfedc rTEV gfedc Strep-tag

gfedc GST

gfedcthioredoxin

gfedc

Other:

gfedc


gfedc


gfedc

Other:

gfedc acTEV gfedc Xpress

Next

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Q 6 4

Q64_1

Q64_2

Q64_3 Q64_3_other

Q 6 5

Q65_4

Q65_3

Q65_1

Q65_2

Q65_5 Q65_5_other

Q 6 6

Q66_1 Q66_6 Q66_3

Q66_4 Q66_11 Q66_8

Q66_2 Q66_5 Q66_13 Q66_13_other

Q66_7 Q66_10 Q66_14 Q66_14_other

Q66_12 Q66_9




The next questions pertain to mammalian expression systems

Considering your usage, how many total mammalian preps do you perform in a typical month?

mammalian preps per month, on average

Do you use a specific expression system for production of proteins in mammalian cells?

nmlkj yes

nmlkj no

Next

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Q 4 0

[SCR IPT ]

Q 4 1


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Which expression system(s) do you use most often with mammalian cells? (Multiple answers may be chosen). Please add any additional expression systems under 'other'. If more than two, please list all separated by commas.

gfedcLacSwitch

gfedc pTet

gfedc RetroXpres

gfedcTet-On

gfedc pTNT

gfedc Ecdysone

gfedcSindbis

gfedcpTARGET

gfedc

Other:

gfedc pcDNA

gfedcLentovirus

gfedc

Other:

If you do not use a specific expression system, what type(s) of vector do you use most often with mammalian cells? (Multiple answers may be chosen).

gfedc

pMam/Neo and related vectors (Clontech)

gfedc

ZapExpress and related vectors (Stratagene)

gfedc

pCl and related vectors (Promega)

gfedc pCEP4 and related vectors (Invitrogen)

gfedc

pcmv/Sport (Invitrogen)

gfedc pQE-TriSystem (Qiagen)

gfedc

pTriEx and related vectors (Novagen)

gfedc

Other:

gfedc

pcDNA 3.1 and related vectors (Promega)

If you use epitope tags for detection and analysis of recombinant proteins in mammalian cells, whichdo you use most often? (Multiple answers may be chosen). Please add any additional epitope tags under 'other'. If more than two, please list all separated by commas.

gfedcV5

gfedc Strep-tag

gfedc His-tag

gfedc

Other:

gfedcT7

gfedc HSV

gfedc Xpress

gfedc

Other:

gfedc

c-myc

gfedchemagglutinin

gfedcglutathione

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Q 4 2

Q42_3 Q42_5 Q42_7

Q42_6 Q42_10 Q42_1

Q42_4 Q42_9 Q42_11 Q42_11_other

Q42_8 Q42_2 Q42_12 Q42_12_other

Q 4 3

Q43_4 Q43_8

Q43_2 Q43_5

Q43_6 Q43_7

Q43_3 Q43_9 Q43_9_other

Q43_1

Q 4 4

Q44_1 Q44_4 Q44_7 Q44_10 Q44_10_other

Q44_2 Q44_5 Q44_8 Q44_11 Q44_11_other

Q44_3 Q44_6 Q44_9




Do you generate stable cell lines for protein expression?

nmlkj Yes

nmlkj No

If so, which expression vector or kit do you use?

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Q 4 5

Q 4 6




If you produce protein from transiently transfected cells, which expressionvector or expression kit, and transfection agent do you use?

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Q 4 7




Finally, please answer a few questions about your self.

How would you best describe your organization?

Select one:

What most closely fits your job description?

Select one:

How many years of experience do you have with protein expression systems?

years

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Q 9 1

Q 9 2

Q 9 3




Please indicate below your primary scientific discipline.

Select one:

Do you work in a core facility that provides protein expression services?

nmlkj Yes, I work in a core faci l ity that provides protein expression services.

nmlkj I work in a core faci l ity which does not provide protein expression services.

nmlkj No, I don't work in a core facil ity.

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Q 9 4

Q 9 5




OK. now please choose your free gift from the following list:

Select one:

Please make sure we have your current contact information by completing the fields below:

First Name, Last Name:

Organization:

Department:

Address:

City, State, Zip:

Country: USA

Telephone: (Not required, but helpful in case of problem delivering gift).

E-mail:

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pr i ze

who




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Thank you for taking time to participate in one of our research surveys.

We expect to begin delivering gifts at the end of the project, or in about 4-8 weeks time.

We look forward to inviting you to participate in another study in the future.

Sincerely,

The PhorTech Team

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Cong ra tu l a t i ons




Sorry, but you must be currently involved with protein expression research to participate in this survey. Please stop now. We hope to invite you to a more appropriate survey in the future.

Best regards,

The PhorTech Team

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2008/2009 msppsa series protein expression … · 2016. 11. 16. · resps' familiarity with...

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