This book provides a decent overview of common laboratory techniques including common procedures and drawbacks. The information is presented at an undergraduate level, but assumes quite a bit of knowledge of basic techniques, such as isoelectric focusing, so would be better called upper level undergraduate. Without considerable background knowledge, this book would not make good self-study material. The sections in the book read like small independent essays. The book is broken down into 15 chapters:
1. Proteomics and the New Biology: This chapter defines what the proteome is, why it should be studied, the tools used, and its applications.
2. The Proteome: Here, the relationships between the proteome and the genome as well as the basic structures of proteins are explored.
3. Overview of Analytical Proteomics: This 3 page 'chapter' provides a flow-chart for proteomics analysis.
4. Analytical Protein and Peptide Separations: This chapter gives overviews of one-dimensional SDS-PAGE, two-dimensional SDS-PAGE, isoelectric focusing (IEF), HPLC, tandem HPLC, and capillary electrophoresis (CE). While it gives decent overviews of the techniques listed, it does a poor job of explaining the underlying principles which govern them.
5. Protein Digestion Techniques: This chapter focuses on the proteases trypsin, Glu-C, cleavage reactants, nonspecific proteases, and cyanogen bromide with a quick rumination on in-gel digestion.
6. Mass Spectrometers for Protein and Peptide Analysis: After what may be the briefest overview of mass spectrometry ever, this chapter turns its attention to MALDI-TOF instrumentation, the TOF mass analysis, benefits and drawbacks to MALDI, ESI tandem MS instrumentation, peptide ions in ESI, tandem mass analysis, triple quadrupole mass analysis, ion-trap mass analysis, automated data acquisition, Q-TOF mass analysis, and Fourier transform-ion cyclotron resonance MS instrumentation. All of this in a scant 20 pages. The overviews are not in depth and do not give a lot of background information.
7. Protein Identification by Peptide Mass Fingerprinting: This chapter explains the analytical approach to identification taken by most software, how to use the software, and how to determine if your result is good. There is no mention of the underlying methods behind the software (hidden Markov chains, information theory, neural nets, etc).
8. Peptide Sequence Analysis by Tandem Mass Spectrometry: This chapter focuses on how to pick out individual peptides from tandem MS data based on the chemical composition of the peptides. This is another very short chapter that would have benefited from being longer.
9. Protein Identification with Tandem Mass Spectrometry Data: This chapter goes over the analytical tools used to identify proteins from the raw data, focusing on sequest. Much like chapter 7, it does not go into detail on how the software works to find the matches.
10. SALSA: An Algorithm for Mining Specific Features of Tandem MS Data: This chapter gives a good introduction to SALSA and another poor explanation of how searching software works.
11. Mining Proteomes: This chapter gives explainations and an analysis of two mining approaches: 2D-SDS-PAGE + MALDI-TOF MS and multidimensional peptide chromatography + LC-tandem MS.
12. Protein Expression Profiling: This chapter explains how to do comparative proteomics with 2D-SDS-PAGE gels using the Melanie(tm) software from the Swiss Institute for Bioinformatics and with LC-MS isotope tags.
13. Identifying Protein-Protein Interactions and Protein Complexes: This chapter covers immunoprecipitation, the two-hybrid yeast system, MS analysis of protein-protein complexes, the baiting approach, and EMSA. The multitude of diagrams makes it easy to understand, even if the methods seem esoteric.
14. Mapping Protein Modifications: This chapter attempts to touch on a few methods of picking out modifications on proteins from MS data. The chapter is pretty disorganised.
15: New Directions in Proteomics: Given that the book was written in 2002, most of this chapter is not new directions, but current technology.
1. Proteomics and the New Biology: This chapter defines what the proteome is, why it should be studied, the tools used, and its applications.
2. The Proteome: Here, the relationships between the proteome and the genome as well as the basic structures of proteins are explored.
3. Overview of Analytical Proteomics: This 3 page 'chapter' provides a flow-chart for proteomics analysis.
4. Analytical Protein and Peptide Separations: This chapter gives overviews of one-dimensional SDS-PAGE, two-dimensional SDS-PAGE, isoelectric focusing (IEF), HPLC, tandem HPLC, and capillary electrophoresis (CE). While it gives decent overviews of the techniques listed, it does a poor job of explaining the underlying principles which govern them.
5. Protein Digestion Techniques: This chapter focuses on the proteases trypsin, Glu-C, cleavage reactants, nonspecific proteases, and cyanogen bromide with a quick rumination on in-gel digestion.
6. Mass Spectrometers for Protein and Peptide Analysis: After what may be the briefest overview of mass spectrometry ever, this chapter turns its attention to MALDI-TOF instrumentation, the TOF mass analysis, benefits and drawbacks to MALDI, ESI tandem MS instrumentation, peptide ions in ESI, tandem mass analysis, triple quadrupole mass analysis, ion-trap mass analysis, automated data acquisition, Q-TOF mass analysis, and Fourier transform-ion cyclotron resonance MS instrumentation. All of this in a scant 20 pages. The overviews are not in depth and do not give a lot of background information.
7. Protein Identification by Peptide Mass Fingerprinting: This chapter explains the analytical approach to identification taken by most software, how to use the software, and how to determine if your result is good. There is no mention of the underlying methods behind the software (hidden Markov chains, information theory, neural nets, etc).
8. Peptide Sequence Analysis by Tandem Mass Spectrometry: This chapter focuses on how to pick out individual peptides from tandem MS data based on the chemical composition of the peptides. This is another very short chapter that would have benefited from being longer.
9. Protein Identification with Tandem Mass Spectrometry Data: This chapter goes over the analytical tools used to identify proteins from the raw data, focusing on sequest. Much like chapter 7, it does not go into detail on how the software works to find the matches.
10. SALSA: An Algorithm for Mining Specific Features of Tandem MS Data: This chapter gives a good introduction to SALSA and another poor explanation of how searching software works.
11. Mining Proteomes: This chapter gives explainations and an analysis of two mining approaches: 2D-SDS-PAGE + MALDI-TOF MS and multidimensional peptide chromatography + LC-tandem MS.
12. Protein Expression Profiling: This chapter explains how to do comparative proteomics with 2D-SDS-PAGE gels using the Melanie(tm) software from the Swiss Institute for Bioinformatics and with LC-MS isotope tags.
13. Identifying Protein-Protein Interactions and Protein Complexes: This chapter covers immunoprecipitation, the two-hybrid yeast system, MS analysis of protein-protein complexes, the baiting approach, and EMSA. The multitude of diagrams makes it easy to understand, even if the methods seem esoteric.
14. Mapping Protein Modifications: This chapter attempts to touch on a few methods of picking out modifications on proteins from MS data. The chapter is pretty disorganised.
15: New Directions in Proteomics: Given that the book was written in 2002, most of this chapter is not new directions, but current technology.
