Proteomics is the analysis of a cell, tissue, or organism's protein content. We also call this the proteome, which you have to find below. The proteome describes the complete set of proteins encoded by a genome. However, just because the genome encodes for all these different proteins, doesn't necessarily mean that those proteins will all be expressed at the same times. Generally, the cell responds to different environmental conditions, and so different proteins are expressed at different times. When studying proteomics, you have to understand that proteomics is very different depending on the condition or timing you're looking at the cell, tissue, or organism. Another interesting thing is that due to protein processing, such as alternative splicing or RNA editing, the proteome is actually much larger than the number of genes that code for proteins. Right? Because a single protein, after it undergoes alternative splicing, can have 5 or 6 different forms called isoforms. This represents 5 or 6 different proteins, encoded by one gene. One gene doesn’t necessarily encode just one protein in humans; through different processing methods, it can encode a variety of proteins.
Several methods have been developed to isolate proteins. One of these is called gel electrophoresis, which I talk about in a cloning video. Gel electrophoresis can separate proteins, as well as DNA and RNA, but in the context of proteomics, we'll focus on proteins. There are a couple of different ways this is done. One is SDS-PAGE, which separates proteins by mass. But there are also other types of gel electrophoresis that can separate proteins by charge. When it is separating proteins by charge, we call it isoelectric focusing. Proteins migrate in the gel to the point where their charge is zero. Typically, this looks like dots of different sizes and some with little tails after them, representing separation by mass and charge. If it’s a negatively charged protein, it will move towards the positive side, and if it’s a positively charged protein, it will move towards the negative side. Each dot eventually reaches an isoelectric focusing point, where its charge is zero. This is because it's sitting in a spot where it no longer wants to move, as it has moved as far as its charge dictates, no longer being drawn to the other side.
There are a variety of different techniques used to identify what proteins exist in a certain sample. One of these is called mass spectrometry. An example of this is tandem mass spectrometry, which separates proteins by mass and charge and can identify the amino acid sequence of the protein being analyzed. By recognizing the peaks of individual amino acids, one can determine the sequence, such as identifying glycine, valine, and leucine, and then matching this sequence to a gene in the genome. Another method is the Protein Microarray. Similar to DNA or RNA microarrays, it detects proteins and protein-to-protein interactions. This method involves antibodies fixed to a plate that bind to the proteins in the sample; those that bind are present in the sample, and those that do not are not present. Both mass spectrometry and protein microarrays are crucial in both biological and chemical techniques.
Having introduced these techniques in the context of proteomics, it is time to move on. While these methods may be more prevalent in chemistry classes, they are essential to understanding various aspects of genetics and biochemistry as well.
