New PDF release: Computational methods for mass spectrometry proteomics

By Ingvar Eidhammer; et al

ISBN-10: 0470512970

ISBN-13: 9780470512975

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Org/tools/) to calculate the pI value for the peptide. 4 Consider the peptide ARTWLCDYEVTKRSEPTVGR. (a) Calculate the GRAVY score for the first windows of length five. htm) to show a hydropathy (hydrophobicity) plot of the whole peptide. 5 Write a program that given the (nominal) mass of a peptide calculates the possible amino acid composition of the peptide. Remember that the mass of a peptide is the sum of the residue masses plus the mass of a water molecule (H2 O). Run the program on the peptide mass 677.

This effect is much more noticeable for whole proteins as their long sequence can be modified several times with several different modifications. For the much shorter peptides, the combinatorial possibilities are more manageable. Also, it is difficult to perform large-scale analysis of intact proteins with top-down proteomics techniques. The bottom-up paradigm is therefore used as the basis for the presentation in this book. For the sake of completeness, an introduction to the top-down paradigm is given in Chapter 17.

Precision Precision is the closeness of agreement between independent measurements obtained by applying the experimental procedure under stipulated conditions. The smaller the random part of the experimental errors which affect the results, the more precise the procedure. A measure of precision is the standard deviation, or a formula based on the standard deviation. When a more precise definition is needed, repeatability or reproducibility is used. Repeatability considers the same method with the same test material under the same conditions (same operator, same apparatus, same laboratory, and after short intervals of time) but reproducibility means under different conditions.

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