By Ingvar Eidhammer; et al
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Additional info for Computational methods for mass spectrometry proteomics
This is not an ideal situation with regard to the separation procedure. The necessary preprocessing of the proteins is achieved by treating them with sodium dodecyl sulfate (SDS), a detergent molecule with a long hydrophobic tail and a negatively charged head. SDS will then: • denature the proteins; and • impart negative charges to the proteins (roughly) proportional to the size of the protein. 1. After being prepared, the resulting negatively charged and denatured proteins are loaded onto the polyacrylamide gel.
Mass spectrometers are general instruments for measuring the masses of the molecules in a sample. However, mass spectrometers are only able to recognize charged molecules, therefore the molecules must be ionized. In proteomics the ionization is commonly achieved by the addition of protons, and more rarely by loss of protons. Hence the mass of the peptide or protein is increased by the nominal mass of 1 Da times the number of charges (protons) in the case of addition, and decreased by the nominal mass of 1 Da times the number of charges in the case of loss of protons.
INSTRUMENT CALIBRATION AND MEASURING ERRORS 27 The value of a measurement can be precise but not accurate, neither of them, or both of them. However, it is not possible to achieve high accuracy without high precision; if the values are not similar to one another, they cannot all be similar to the correct value. If the value from a measurement is both accurate and precise, it is often said to be valid. 455. 425}. The first instrument has high precision, but low accuracy; the other has higher accuracy, but lower precision.