Clinical and Biomedical Applications of Proteomics

Hochstrasser, Denis F.

doi:10.1007/978-3-662-03493-4_8

Cited by 38 publications

(5 citation statements)

References 99 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Because the number of proteins can strongly exceed the number of genes, the task of assigning functional roles to all of these proteins is a formidable task. Although some simplification is offered by the fact that a typical eukaryotic cell may express only 5000–10,000 genes (Hochstrasser, 1997), there is still clearly a need for systematic ways of identifying smaller groups of genes/proteins that are related by function. One of the premises of functional proteomics is that this goal can be achieved via functional stimulation or perturbation of the complex cellular networks.…”

Section: Why Functional Proteomics?mentioning

confidence: 99%

Perspectives for mass spectrometry and functional proteomics

Godovac‐Zimmermann

Brown²

2001

Mass Spectrom. Rev.

262

185

View full text Add to dashboard Cite

I.Introduction2II.Why Functional Proteomics?3 A. The Complementarity of Genomics and Proteomics3 B. Genotypes and Protein Phenotypes3 C. New Views of Biological Function5 D. The Role of Mass Spectrometry6 E. Current General Areas of Proteome Research7 1. Mapping of Total Cellular Proteins7 2. Subcellular Complexes and Organelles10 3. Protein Phenotypes and Function13 F. The Need for and Utility of Functional Proteomics15 1. Definition of Functional Proteomics.15 2. A New Biology—Networks, Fluxes, and Dynamics at the Molecular Level16 3. The Importance of Assigning Gene Functions in Context16 4. Practical Advantages of Functional Proteomics17III.Recent Applications of Functional Proteomics and Mass Spectrometry17 A. Changes in Cellular Environment17 B. Direct Observation of Growth Factor Signal Transduction19 C. Protein Synthesis Following Directed Cellular Perturbation22 D. Directed Measurement of Functional Classes of Proteins24 E. Global Detection of Specific Types of Functional Activities in Cells25 F. Investigating the Function of Individual Proteins26 G. Summary29IV.Technical Advances for Functional Proteomics29 A. “Total” Proteins29 B. Display Methodologies31 C. Quantification Methods33 1. Chemical Staining33 2. Antibody‐Based Detection Methods33 3. New Multi‐Photon Detection Methods for Detection of Radioactive Labels34 D. Implications for Automation34V.Perspectives36 A. Directions for Functional Proteomics36 1. Studies of Cells in Culture36 2. Single Cells36 3. Tissue Samples37 4. Medical and Pharmaceutical Themes37 5. Comparative Proteomics37 B. Perturbation Methods—The Importance of Time Scales, Kinetics, and Fluxes38 C. The “Virtual Proteome”39 D. Constructing the “Virtual Proteome”: Community‐Based Proteomics42 1. Standards for Display Maps of the Proteome43 2. Standards for Mass Spectrometric Identification of Proteins43 3. Databases44 E. Implications for Mass Spectrometry45 1. Sensitivity and Functional Proteomics45 2. Phenotypic Characterization of Proteins46 3. Automated Analysis of MS Data in Proteomics47 F. Conclusion48Acknowledgments48References48

show abstract

Section: Why Functional Proteomics?mentioning

confidence: 99%

Perspectives for mass spectrometry and functional proteomics

Godovac‐Zimmermann

Brown²

2001

Mass Spectrom. Rev.

262

185

View full text Add to dashboard Cite

show abstract

“…There is already a vast body of literature applying proteomics in many different areas of clinical and biochemical interest and in the study of the pathogenesis, development, prevention, and treatment of a wide range of diseases [1]. …”

Section: Introductionmentioning

confidence: 99%

“…Proteomics is a relatively new but rapidly maturing discipline within life science research for understanding the biology of an organism via the large-scale study of the proteins expressed by the organism. There is already a vast body of literature applying proteomics in many different areas of clinical and biochemical interest and in the study of the pathogenesis, development, prevention, and treatment of a wide range of diseases [ 1 ].…”

Section: Introductionmentioning

confidence: 99%

Computational Methods for Protein Identification from Mass Spectrometry Data

McHugh¹,

Arthur²

2008

PLoS Comput Biol

View full text Add to dashboard Cite

Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology.

show abstract

“…11). Furthermore, the broad range of protein solubility makes it nearly impossible to detect a complete proteome in a 2-DE gel, since poorly soluble and low abundant proteins are lost [21]. Despite the use of tedious protocols for fractionated detergent extractions, it is still impossible to detect 10-15% of total proteins; vice versa, major abundant and easily soluble proteins like albumin and immunoglobulin G (IgG) are too dominant in a gel, thereby abrogating a sensitive analysis.…”

Section: -De and Protein Identificationmentioning

confidence: 99%

Design of proteome-based studies in combination with serology for the identification of biomarkers and novel targets

Seliger

Kellner

2002

Proteomics

View full text Add to dashboard Cite

Recently proteome analysis has rapidly developed in the post-genome era and is now widely accepted as a complementary technology to genetic profiling. The improvement in the technology of both two-dimensional electrophoresis (2-DE) analysis as well as protein identification has made proteomics a valuable and powerful tool to study human diseases. A combination of conventional proteome analysis with serology has been developed as a promising experimental approach for the discovery of serological markers in different malignancies. However, the design of proteome-based studies has to be carefully performed since there are a number of critical needs for systematic and reproducible proteome analysis. In particular, the selection of tissue and its preparation represent an important step in proteome analysis. Besides the preparation of protein samples, the 2-DE and protein identification is a further critical issue. So far proteome-based technologies have been successfully used in tumor immunnology for the identification of tumor-specific autoantigens. Similarly, this technology has been employed for the detection of virulence factors, antigens and vaccine candidates in infectious diseases, as well as for the identification of diagnostic and prognostic markers, suggesting that proteome-based analysis is a promising tool for the identification of prognostic, diagnostic markers as well as for novel therapeutic targets which could be used for treatment of diseases. The integration of proteome-based approaches with data from genomic or genetic profiling will lead to a better understanding of different diseases, which will then contribute to the direct translation of the research findings into clinical practice.

show abstract

Clinical and Biomedical Applications of Proteomics

Cited by 38 publications

References 99 publications

Perspectives for mass spectrometry and functional proteomics

Perspectives for mass spectrometry and functional proteomics

Computational Methods for Protein Identification from Mass Spectrometry Data

Design of proteome-based studies in combination with serology for the identification of biomarkers and novel targets

Contact Info

Product

Resources

About