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Computational and Statistical Methods for Protein by Ingvar Eidhammer

By Ingvar Eidhammer

The definitive creation to information research in quantitative proteomics

This e-book presents the entire useful wisdom approximately mass spectrometry established proteomics equipment and computational and statistical methods to pursue the making plans, layout and research of quantitative proteomics experiments. The author’s rigorously built procedure permits readers to simply make the transition into the sector of quantitative proteomics. via targeted descriptions of wet-lab equipment, computational techniques and statistical instruments, this ebook covers the total scope of a quantitative test, permitting readers to procure new wisdom in addition to performing as an invaluable reference paintings for extra complex readers.

Computational and Statistical equipment for Protein Quantification via Mass Spectrometry:

  • Introduces using mass spectrometry in protein quantification and the way the bioinformatics demanding situations during this box will be solved utilizing statistical equipment and numerous software program programs.
  • Is illustrated through loads of figures and examples in addition to a number of exercises.
  • Provides either transparent and rigorous descriptions of equipment and approaches.
  • Is completely listed and cross-referenced, combining the strengths of a textual content e-book with the application of a reference work.
  • Features certain discussions of either wet-lab ways and statistical and computational methods.

With transparent and thorough descriptions of many of the tools and techniques, this publication is available to biologists, informaticians, and statisticians alike and is geared toward readers around the educational spectrum, from complex undergraduate scholars to put up doctorates getting into the field.

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4 Mass spectrometry and protein identification The use of mass spectrometry is now the dominant approach for protein quantification. In most protein quantification experiments the identity of the proteins is unknown, and protein identification is necessary. This chapter provides a brief overview of the principles of using mass spectrometry for protein identification and characterization. More extensive introductions can be found elsewhere, for example in Eidhammer et al. (2007). Various protein properties are used in protein identification, perhaps most important is the mass.

For each peptide we have three alternatives: 1. The peptide comes from a protein whose sequence is in D. 2. The peptide comes from a protein whose sequence is homologous to a sequence in D. 3. The peptide comes from an unknown protein, with no homologue in D. Each of the cases above may include modifications, the spectrum may therefore come from a peptide that is modified. In principle, the search is performed by comparing each experimental spectrum to the theoretical peptides (resulting from in silico digestion of the database sequences), and identifying the peptides resulting in the best match(es).

3 illustrates the main principles of mass spectrometry. Suppose that we have a sample of three peptides (a, b, c), with nominal masses a: 680, b: 481, c: 400. Assume further that some of the peptides become singly charged, and some doubly charged, while all b peptides are singly charged, and all c peptides doubly charged. 3. 3 The main principles of mass spectrometry. In the ionization source, the sample components are transferred to gas phase and acquire their charges. In the mass analyzer the components are separated according to their m/z values before hitting the detector.

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