Introduction to proteomic data analysis
Last updated
Last updated
While DNA encodes the "instructions of life", the proteins derived from the translation of RNA molecules are the entities that put these instructions into practice. So far in the class we have focused on DNA and protein strings without discussing how scientists have figured out what these strings are. In this chapter, we will focus on one experimental approach that can be used to uncover the amino-acid sequence of proteins.
We will start by focusing on a special type of proteins, cyclical non-ribosomal peptides. They are called cyclical because the protein is organized into a circular structure. Many of these molecules are used as antibiotics, anti-cancer drugs, tumor suppressors, and in other applications.
One of the experimental processes used to determine the sequence of amino-acids forming one of these non-ribosomal peptides is called mass spectrometry, and is described in more detail below.
Mass spectrometry is an analytic technique that is used to measure the mass to charge ratio (m/z) of molecules. At a very high level view, a mixture of molecules is ionized (thereby providing them with a charge, which enables their manipulation by electric currents). These charged molecules are then "sprayed" into a chamber, where electric and/or magnetic fields are applied perpendicularly to the direction in which the particles move. The combination of the speed with which each molecule moves through the chamber, its mass to charge ratio, and the strength of the field applied determine how much the trajectory of the particle deviates from a straight line. The mass of each particle determines its inertia, while the charge of each particle determines the force exerted to it by the field, resulting in a deviation that is inversely proportional to the mass to charge ratio of each particle. Heavy particles with low charges only deviate a little, while low-mass particles that are heavily charged deviate the most.
A detector at the end of the chamber captures the particles and measures both their distance from the center and the abundance of the particles "hitting" a particular location in the detector, yielding signals such as that shown below.
