Metabolome Analysis: An Introduction / Edition 1

Hardcover (Print)
Buy New
Buy New from
Used and New from Other Sellers
Used and New from Other Sellers
from $87.96
Usually ships in 1-2 business days
(Save 18%)
Other sellers (Hardcover)
  • All (4) from $87.96   
  • New (3) from $87.96   
  • Used (1) from $87.96   


Providing information on the main approaches for the analysis of metabolites, this textbook:

  • Covers basic methodologies in sample preparation and separation techniques, as well as the most recent techniques of mass spectrometry.
  • Differentiates between primary and secondary metabolites.
  • Includes four chapters discussing successful metabolome studies of different organisms.
  • Highlights the analytical challenges of studying metabolites.
  • Illustrates applications of metabolome analysis through the use of case studies.
Read More Show Less

Editorial Reviews

From the Publisher
"Overall, this book provides a great introduction to metabolomics and at a retail price of approximately $75, it has great value. The intended audience for this book includes new metabolomics practitioners and undergraduate/graduate students." (J Am Soc Mass Spectrom, 2007)
Read More Show Less

Product Details

Meet the Author

SILAS G. VILLAS-BÔAS, PHD, is a Research Scientist at AgResearch Limited in New Zealand.

UTE ROESSNER, PHD, is a Post-Doctoral Fellow at the Australian Centre for Plant Functional Genomics at the University of Melbourne, Australia.?

MICHAEL A. E. HANSEN, PHD, is a Post-Doctoral Fellow at BioCentrum-DTU, Technical University of Denmark.

JØRN SMEDSGAARD, PHD, is an Associate Professor at the Center for Microbial Biotechnology, BioCentrum-DTU at the Technical University of Denmark.

JENS NIELSEN, PROFESSOR, Dr. techn., PHD, is the Director of the Center for Microbial Biotechnology at the Technical University of Denmark.

Read More Show Less

Table of Contents




1 Metabolomics in Functional Genomics and Systems Biology.

1.1 From genomic sequencing to functional genomics.

1.2 Systems biology and metabolic models.

1.3 Metabolomics.

1.4 Future perspectives.

2 The Chemical Challenge of the Metabolome.

2.1 Metabolites and metabolism.

2.2 The structural diversity of metabolites.

2.2.1 The chemical and physical properties.

2.2.2 Metabolite abundance.

2.2.3 Primary and secondary metabolism.

2.3 The number of metabolites in a biological system.

2.4 Controlling rates and levels.

2.4.1 Control by substrate level.

2.4.2 Feedback and feedforward control.

2.4.3 Control by “pathway independent” regulatory molecules.

2.4.4 Allosteric control.

2.4.5 Control by compartmentalization.

2.4.6 The dynamics of the metabolism—the mass fl ow.

2.4.7 Control by hormones.

2.5 Metabolic channeling or metabolons.

2.6 Metabolites are arranged in networks that are part of a cellular interactome.

3 Sampling and Sample Preparation.

3.1 Introduction.

3.2 Quenching—the first step.

3.2.1 Overview on metabolite turnover.

3.2.2 Different methods for quenching.

3.2.3 Quenching microbial and cell cultures.

3.2.4 Quenching plant and animal tissues.

3.3 Obtaining metabolites from biological samples.

3.3.1 Release of intracellular metabolites.

3.3.2 Structure of the cell envelopes—the main barrier to be broken.

3.3.3 Cell disruption methods.

3.3.4 Nonmechanical disruption of cell envelopes.

3.3.5 Mechanical disruption of cell envelopes.

3.4 Metabolites in the extracellular medium.

3.4.1 Metabolites in solution.

3.4.2 Metabolites in the gas phase.

3.5 Improving detection via sample concentration.

4 Analytical Tools.

4.1 Introduction.

4.2 Choosing a methodology.

4.3 Starting point—samples.

4.4 Principles of chromatography.

4.4.1 Basics of chromatography.

4.4.2 The chromatogram and terms in chromatography.

4.5 Chromatographic systems.

4.5.1 Gas chromatography.

4.5.2 HPLC systems.

4.6 Mass spectrometry.

4.6.1 The mass spectrometer—an overview.

4.6.2 GC-MS—the EI ion source.

4.6.3 LC-MS—the ESI ion source.

4.6.4 Mass analyzer—the quadrupole.

4.6.5 Mass analyzer—the ion-trap.

4.6.6 Mass analyzer—the time-of-fl ight.

4.6.7 Detection and computing in MS.

4.7 The analytical work-fl ow.

4.7.1 Separation by chromatography.

4.7.2 Mass spectrometry.

4.7.3 General analytical considerations.

4.8 Data evaluation.

4.8.1 Structure of data.

4.8.2 The chromatographic separation.

4.8.3 Mass spectral data.

4.8.4 Exporting data for processing.

4.9 Beyond the core methods.

4.9.1 Developments in chromatography.

4.9.2 Capillary electrophoresis.

4.9.3 Tandem MS and advanced scanning techniques.

4.9.4 NMR spectrometry.

4.10 Further reading.

5 Data Analysis.

5.1 Organizing the data.

5.2 Scales of measurement.

5.2.1 Qualitative data.

5.2.2 Quantitative data.

5.3 Data structures.

5.4 Preprocessing of data.

5.4.1 Calibration of data.

5.4.2 Combining profi le scans.

5.4.3 Filtering.

5.4.4 Centroid calculation.

5.4.5 Internal mass scale correction.

5.4.6 Binning.

5.4.7 Baseline correction.

5.4.8 Chromatographic profi le matching.

5.5 Deconvolution of spectroscopic data.

5.6 Data standardization (normalization).

5.7 Data transformations.

5.7.1 Principal component analysis.

5.7.2 Fisher discriminant analysis.

5.8 Similarities and distances between data.

5.8.1 Continuous functions.

5.8.2 Binary functions.

5.9 Clustering techniques.

5.9.1 Hierarchical clustering.

5.9.2 k-means clustering.

5.10 Classifi cation techniques.

5.10.1 Decision theory.

5.10.2 k-nearest neighbor.

5.10.3 Tree-based classifi cation.

5.11 Integrated tools for automation, libraries, and data evaluation.


6 Yeast Metabolomics: The Discovery of New Metabolic Pathways in Saccharomyces cerevisiae.

6.1 Introduction.

6.2 Brief description of the methodology used.

6.2.1 Sample preparation.

6.2.2 The analysis.

6.3 Early discoveries.

6.4 Yeast stress response gives evidence of alternative pathway for glyoxylate biosynthesis in S. cerevisiae.

6.5 Biosynthesis of glyoxylate from glycine in S. cerevisiae.

6.5.1 Stable isotope labeling experiment to investigate glycine catabolism in S. cerevisiae.

6.5.2 Data leveraged for speculation.

7 Microbial Metabolomics: Rapid Sampling Techniques to Investigate Intracellular Metabolite Dynamics—An Overview.

7.1 Introduction.

7.2 Starting with a simple sampling device proposed by Theobald et al. (1993).

7.3 An improved device reported by Lange et al. (2001).

7.4 Sampling tube device by Weuster-Botz (1997).

7.5 Fully automated device by Schaefer et al. (1999).

7.6 The stopped-fl ow technique by Buziol et al. (2002).

7.7 The BioScope: a system for continuous-pulse experiments.

7.8 Conclusions and perspectives.

8 Plant Metabolomics.

8.1 Introduction.

8.2 History of plant metabolomics.

8.3 Plants, their metabolism and metabolomics.

8.3.1 Plant structures.

8.3.2 Plant metabolism.

8.4 Specifi c challenges in plant metabolomics.

8.4.1 Light dependency of plant metabolism.

8.4.2 Extraction of plant metabolites.

8.4.3 Many cell types in one tissue.

8.4.4 The dynamical range of plant metabolites.

8.4.5 Complexity of the plant metabolome.

8.4.6 Development of databases for metabolomics-derived data in plant science.

8.5 Applications of metabolomics approaches in plant research.

8.5.1 Phenotyping.

8.5.2 Functional genomics.

8.5.3 Fluxomics.

8.5.4 Metabolic trait analysis.

8.5.5 Systems biology.

8.6 Future perspectives.

9 Mass Profi ling of Fungal Extract from Penicillium Species.

9.1 Introduction.

9.2 Methodology for screening of fungi by DiMS.

9.2.1 Cultures.

9.2.2 Extraction.

9.2.3 Analysis by direct infusion mass spectrometry.

9.3 Discussion.

9.3.1 Initial data processing.

9.3.2 Metabolite prediction.

9.3.3 Chemical diversity and similarity.

9.4 Conclusion.

10 Metabolomics in Humans and Other Mammals.

10.1 Introduction.

10.2 A brief history of mammalian metabolomics.

10.3 Sample preparation for mammalian metabolomics studies.

10.3.1 Working with blood.

10.3.2 Working with urine.

10.3.3 Working with cerebrospinal fl uid.

10.3.4 Working with cells and tissues.

10.4 Sample analysis.

10.4.1 GC-MS analysis of urine, plasma, and CSF.

10.4.2 LC-MS analysis of urine, blood, and CFS.

10.4.3 NMR analysis of CSF, urine, and blood.

10.5 Applications.

10.5.1 Identifi cation and classifi cation of metabolic disorders.

10.6 Future outlook.


Read More Show Less

Customer Reviews

Be the first to write a review
( 0 )
Rating Distribution

5 Star


4 Star


3 Star


2 Star


1 Star


Your Rating:

Your Name: Create a Pen Name or

Barnes & Review Rules

Our reader reviews allow you to share your comments on titles you liked, or didn't, with others. By submitting an online review, you are representing to Barnes & that all information contained in your review is original and accurate in all respects, and that the submission of such content by you and the posting of such content by Barnes & does not and will not violate the rights of any third party. Please follow the rules below to help ensure that your review can be posted.

Reviews by Our Customers Under the Age of 13

We highly value and respect everyone's opinion concerning the titles we offer. However, we cannot allow persons under the age of 13 to have accounts at or to post customer reviews. Please see our Terms of Use for more details.

What to exclude from your review:

Please do not write about reviews, commentary, or information posted on the product page. If you see any errors in the information on the product page, please send us an email.

Reviews should not contain any of the following:

  • - HTML tags, profanity, obscenities, vulgarities, or comments that defame anyone
  • - Time-sensitive information such as tour dates, signings, lectures, etc.
  • - Single-word reviews. Other people will read your review to discover why you liked or didn't like the title. Be descriptive.
  • - Comments focusing on the author or that may ruin the ending for others
  • - Phone numbers, addresses, URLs
  • - Pricing and availability information or alternative ordering information
  • - Advertisements or commercial solicitation


  • - By submitting a review, you grant to Barnes & and its sublicensees the royalty-free, perpetual, irrevocable right and license to use the review in accordance with the Barnes & Terms of Use.
  • - Barnes & reserves the right not to post any review -- particularly those that do not follow the terms and conditions of these Rules. Barnes & also reserves the right to remove any review at any time without notice.
  • - See Terms of Use for other conditions and disclaimers.
Search for Products You'd Like to Recommend

Recommend other products that relate to your review. Just search for them below and share!

Create a Pen Name

Your Pen Name is your unique identity on It will appear on the reviews you write and other website activities. Your Pen Name cannot be edited, changed or deleted once submitted.

Your Pen Name can be any combination of alphanumeric characters (plus - and _), and must be at least two characters long.

Continue Anonymously

    If you find inappropriate content, please report it to Barnes & Noble
    Why is this product inappropriate?
    Comments (optional)