1

Next-Generation Mass Spectrometry:Technology Advances and Applications

K. John Morrow, Jr., Ph.D.

Advances in biomedical instrumentation are enabling a new perspective that could not have been achieved even a decade ago. Mass spectrometry is the most significant and far reaching of these developments, allowing the generation of data in the medical sciences that brings new insights into critical questions. This report analyzes:

Physical principles and analytical applications of mass spectrometry•

The role of mass spectrometry in genomics, proteomics, metabolomics, and lipidomics•

Advances in mass spectrometry instrumentation and methods•

Current and emerging applications of mass spectrometry •

Future prospects for the mass spectrometry industry •

Also included are interviews with mass spectrometry experts in the academic and private sectors

Mass spectrometry is a highly sophisticated instrumentation technology that has emerged as the premier method for the analytical definition of biomolecules. This newly defined role has been the result of significant improvements in these instruments, combined with the introduction of a number of new approaches to preparation and separation of the target molecules.

Next-Generation Mass Spectrometry: Technology Advances and Applications focuses on the role that mass spectrometry has played in the advance of biotechnology. In recent years, it has morphed from a costly and cumbersome machine, sequestered within the domain of analytical chemistry, to an amiable companion, accessible both financially and technically to laboratories that are not specialized in its many uses and applications. Given the limitations of large and complex instruments of the past, it is clear that the direction of evolution of these devices will be toward greater specialization with attendant simplification. This process is well underway, and in this report we examine some of the most imaginative directions in the engineering of new generations of mass spectrometers.

INSIGHT PHARMA REPORTS 250 First Avenue Suite 300 n Needham, MA 02494 n 781.972.5444 n InsightPharmaReports.comA Division of Cambridge Healthtech Institute

ANEW! Interactive Format Now Available

2

We briefly review the history of mass spectrometry and consider (in a non-mathematical framework) the underlying physical principles that dictate the construction and limitations of mass spectrometers. Today mass spectrometry is characterized by rapid advances in technology, driven by manufacturers’ engineering applications. It is acknowledged to be the third most powerful spectral technique in the structural elucidation of unknown organic compounds, trumped only by X-ray diffraction and NMR spectroscopy. But it offers the unsurpassed features of easy coupling to gas-phase and liquid-phase separation techniques, in addition to its extremely high sensitivity and low sample consumption.

In reviewing mass spectrometry instrumentation, Next-Generation Mass Spectrometry: Technology Advances and Applications considers hardware designed to move fragile molecules into a gaseous ionized state, where they can be subsequently analyzed. These include electrospray ionization, matrix-assisted laser desorption/ionization (MALDI), and surface-enhanced laser desorption/ionization (SELDI). Following the vaporization/ionization procedure, the sample is introduced into the mass analyzer, of which there are many types, as presented in this report. As evidenced by our discussion, analyzers are numerous and designed for a variety of applications. We review the more significant applications of mass spec technology, including within the areas of proteomics, genomics, metabolomics, lipidomics, forensics, environmental monitoring, and data analysis.

Finally, we draw conclusions about the industry’s future prospects. Mass spectrometry, as the leading technology for the characterization of macromolecules, is likely in the coming years to produce breakthrough advances in the diagnosis and understanding of a host of recalcitrant diseases.

About the AuthorK. John Morrow, Jr., PhD is a writer and consultant for the biotechnology industry. He obtained his PhD in genetics from the University of

Washington in Seattle, and completed his training with post-doctoral studies in Italy at the Universitá di Pavia and in Philadelphia at the Fox Chase Cancer Institute. He has held faculty positions at the University of Kansas and at Texas Tech University Health Sciences Center. His writings include over 200 peer-reviewed journal papers, non–peer-reviewed coverage of the biotechnology industry, books, and marketing reports. A number of companies, including Meridian Bioscience, Affitech, Henderson-Morley Biotechnology, Brandwidth Communications, and Emergent Technologies have taken advantage of his consultancy services, provided through Newport Biotechnology Consultants. He resides in Newport, KY.

Included in this report: •75 pages•11 Tables & Figures•8 Interviews•Exclusivecontentnotavailablein

any other research report.

Plus! •InsightPharmaReportspdfsareinteractive–includingnavigation,search,bookmarks,

download options, and additional layered content. Click here to view a sample.•AccesstoInsightPharmaReportsInteractive-acuttingedgetoolboxforreportbuyers!

This feature allows faster access, better searches & navigation; create custom output and 9 language translations. Click here for a demo.

3

Sample Figure

Two-Dimensional Electrophoresis

pI

High

M.W.

Low

(1) IEF or IPG17-72 hr

(2) SDS-PAGE6 hr

Figure 3.1. Separating Proteins by Electrophoresis

Source: Insight Pharma Reports

(-)

(+)

(-)

(+)

4

Executive SummaryChApter 1

Introduction1.1. Scientific Background History of MS

Physical Principles

Analytical Applications

1.2. The Role of Mass Spectrometry in Genomics/ Proteomics/ Metabolomics/ Lipidomics1.3. Conclusions: A Versatile Analytical Tool

ChApter 2

Mass Spectrometry Instruments2.1. Electrospray Ionization (ESI)2.2. Matrix-Assisted Laser Desorption/Ionization (MALDI)2.3. SELDI-TOF2.4. Mass Analyzers Quadrupole Mass Filter

Quadrupole Ion Trap

Gas Chromatograph-Quadrupole Mass Spectrometer

Time-of-Flight (TOF) Mass Analyzer

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Tandem Mass Spectrometer (MALDI-TOF/TOF)

Fourier-Transform Ion Cyclotron Resonance Mass Analyzer

Hybrid Instruments

Liquid Chromatography (LC)

Gas Chromatography (GC)

LC/MS

Liquid Chromatography Combined with Tandem Mass Spectrometry (LC/MS/MS)

LTQ Orbitrap and Synapt G2 Systems

Magnetic Sector MS

2.5. Fragmentation Methods Tandem Mass Spectrometry MS/MS/MS, MS3, MSn

Ion Trap

Isotope-Coded Affinity Tagging (ICAT)

Isobaric Tab for Relative and Absolute Quantitation (iTRAQ)

Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC)

Tandem Mass Spectrometry (MS/MS)

Collision-Induced Dissociation (CID)

Electron Capture Dissociation (ECD)

Electron Transfer Dissociation (ETD)

ChApter 3

Instruments Used in Conjunction with Mass Spectrometry3.1. Two-Dimensional Gel Electrophoresis3.2. Two-Hybrid Analysis3.3. Protein Microarrays3.4. Protein Database Search Engines

ChApter 4

Applications of Mass Spectrometry Technology4.1. Proteomics Early Investigations Fail to Deliver

A Re-evaluation of the Discovery Process

Multiplex Assays for Proteins

The Problem of Dynamic Range

MudPIT: A Powerful New Discovery Tool

Report Contents

5

4.2. Genomics New Sequencing Technologies Drive Genomics Advances

Findings Arise From Genome Studies

Personalized Cancer Therapies

4.3. Metabolomics4.4. Lipidomics4.5. Environmental Monitoring4.6. Forensics4.7. Sampling4.8. Sample Preparation4.9. Analysis of Impurities Using Mass Spec

ChApter 5

Conclusions, Future Prospects5.1. Systems Biology and Mass Spectrometry5.2. Roadblocks and Challenges in Pursuit of Systems Biology 5.3. A New Perspective on Mass Spectrometry Instrumentation5.4. The Mass Spec Industry Today5.5. Into the Blue, with Caveats

ChApter 6

Interviews with Academic and Private Sector Experts6.1. Dr. Ruedi Aebersold, Professor, Institute of Molecular Sys-tems Biology, Eidgenössische Technische Hochschule Zürich6.2. Dr. R. Graham Cooks, PhD, Professor, Purdue University, Lafayette, IN6.3. Dr. Srinivas Iyer, Research Scientist, Los Alamos National Laboratory, Los Alamos, NM6.4. Dr. Vathany Kulasingam, PhD, Clinical Biochemist and As-sistant Professor, Department of Clinical Biochemistry, University of Toronto6.5. Emanuel F. Petricoin, PhD, Professor and Co-Director, Center for Applied Proteomics and Molecular Medicine, George Mason University6.6. Dr. Ralph Schiess, Institute of Molecular Systems Biology, ETH Zürich6.7. Dr. Ravinder Singh, PhD, Director, Mass Spectrometry Facility, The Mayo Clinic, Rochester, MN6.8. Dr. Klaus Weinberger, CSO, BIOCRATES Life Sciences

References

6

tABLeTable 3.1. A List of Some Popular Peptide Mass Fingerprinting (PMF) Software Packages

FIGUreSFigure 1.1. Components of a Mass Spectrometry InstrumentFigure 2.1. Schematic of an Electrospray Ionization (ESI) Interface Figure 2.2. Schematic of a MALDI Instrument Figure 2.3. The Experimental Steps in SELDI-TOF Figure 2.4. A Quadrupole System Figure 2.5. Time-of-Flight Mass AnalyzerFigure 2.6. Liquid Chromatography with Mass Spectrometry Detection (LC-MS)Figure 2.7. A Schematic of a Sector Mass Spectrometer (‘BE’ geometry) Figure 3.1. Separating Proteins By ElectrophoresisFigure 4.1. A Representation of the MudPIT Technique

7

INSIGHT PHARMA REPORTS 250 First Avenue Suite 300 n Needham, MA 02494 n 781.972.5444 n InsightPharmaReports.comA Division of Cambridge Healthtech Institute

Life Science Reports You Can Rely OnAdvance your knowledge with Insight Pharma Reports’ collection of published reports that provide timely, insightful, and concise analysis on specific topics for your drug development needs. The reports help professionals meet the need to stay abreast of the latest advances in pharmaceutical R&D, their potential applications and business impacts, and their current and future position in the marketplace.

An Essential Collection of Timely & Concise Reports Analyzing the Technologies, Markets, and Strategic Issues Driving R&D Productivity

Newly Published Reports - Click for Complete Details:Next Generation Sequencing Generates Momentum: Markets Respond to Technology and Innovation Advances

Multitargeted Therapies: Promiscuous Drugs and Combination TherapiesCommercializing Biomarkers in Therapeutic and Diagnostic ApplicationsMonoclonal Antibodies in the Pipeline: A Segment of Major Growth

Molecular Diagnostics: Double-Digit Growth Anticipated

Advanced Drug Delivery Technologies: Enabling Drug Reformulations and Administration Routes

RNAi Therapeutics: Second-Generation Candidates Build Momentum

Strategic Alliances: Synergistic Path to Value Creation

Therapeutic Protein Production: A Changing Landscape

Cloud Computing in Life Sciences R&DThe Antiviral Pipeline: HIV, HCV, and Influenza

Visit InsightPharmaReports.com for other available reports.[Corporate subscriptions: Contact David Cunningham, Global Report Sales, 781-972-5472

“CHI’s Insight Pharma Reports are cost-effective and a reliable source of information about the markets we serve.The reports allow us to keep on top of developments in this rapidly moving field.”

Donald N. Halbert, Ph.D., EVP of R&D, Iconix Bioscience

8

Introducing Insight Pharma Reports Interactive - a cutting-edge tool box for report buyers!

Follow Insight Pharma Reports

INSIGHT PHARMA REPORTS 250 First Avenue Suite 300 n Needham, MA 02494 n 781.972.5444 n InsightPharmaReports.comA Division of Cambridge Healthtech Institute

•Advancedfunctionalityforfasteraccesstoreportcontent by taking you straight to the paragraph, table or graph of interest.

•Intuitivesearch,interpret,andinteractfunctionsallow you to create your own custom output.

•Powerfulone-clickapps.allowyoutonavigateandextract all the pertinent information you need from across your entire report portfolio

•Translatereportsinto9languages

Click here to test drive Insight Pharma Reports Interactive and explore our current portfolio of report titles!

A fully searchable listing of the Insight Pharma Report categories helps you find the report that fits your needs.

Sample of a downloadable chart within the Insight Pharma Report. All charts and figures can be downloaded in a number of formats.

AFREE Demo at InsightPharmaReports.com

9

About Insight Pharma ReportsChI’s Insight pharma reports are written by experts who collaborate with CHI to provide a series of reports that evaluate the salient trends in pharmaceutical technology, business, and therapy markets.

Insight Pharma Reports are used by senior decision makers at life sciences companies to keep abreast of the latest advances in pharmaceutical R&D, their potential applications and business impacts. Our clients include the top 50 pharmaceutical companies, top 100 biotechnology companies, and top 100 vendors of life science products and services. Typical purchasers are managers, directors, and VPs in business development, discovery research, clinical development, strategic planing, portfolio management, new product planning, and marketing.

Insight pharma reports offer:Current Information and analysis of R&D technologies, therapeutic markets, and critical •business issues.Analysis of the probaility of success for various applications of each technology.•Expert insight based on interviews with key personnel in companies at the forefront •of technological advances who share their views on their technology’s current status, applications, future direction, and market environment.

RELATED REPORT:

Therapeutic Protein Production: A Changing LandscapeWe examine the implications of advances in upstream and downstream operations used in the production of therapeutic proteins. We consider the impact of global competition, lower barriers to entry, the shift in the production bottleneck from upstream to downstream unit operations, as well as likely shifts impacting the production outlook over the next 5 years. Some of the topics highlighted in this report include:

pAreXeL’s Bio/pharmaceutical r&D Statistical Sourcebook 2010/2011 is the leading resource for statistics, trends and proprietary market intelligence and analysis on the biopharmaceutical industry. For more information, visit www.barnettinternational.com or call 800-856-2556

CLICK BELOW TO RECEIVE A FREE SUBSCRIPTION TO:

BIOMARKER & DIAGNOSTICBREAKTHROUGHS

BIOMARKER & DIAGNOSTICBREAKTHROUGHS

Report PricingSingle User $3,195Single-Site $3,995Multi-Site $9,995

To Order InsightPharmaReports.comPhone: 781.972.5444Email: rlaraia@healthtech.com

Mail: Cambridge Healthtech Institute Rose LaRaia 250 First Avenue, Suite 300 Needham, MA 02494

Call for details on our corporate subscriptions; contact David Cunningham at 781-972-5472 or cunningham@healthtech.com

(Print copies are available on request, with purchase. Call 781-972-5444)

RELATED CAMBRIDGE HEALTHTECH INSTITUTE PRODUCTS:

BARNETTEDUCATIONALSERVICES

EDUCATIONALSERVICES

BARNETT

RELATED CONFERENCES:

For more information on related conferences, visit: Healthtech.com

Pros and cons of animal cell culture•Development of alternative production cell •linesImprovement of protein production per •volume of culture mediaImpact of disposables on cost and •availability of proteins

Appearance of bottlenecks on the •downstream side of productionThe shift away from capital spending on •fixed, reusable infrastructureHow to tackle biosimilar regulatory •questionsDimensions of Asian and EU competition•