 Dear students, in this module I am going to review with you the protein sequencing chapter. You know that the two techniques that are commonly employed in protein sequences include the Edmund degradation and mass spectrometry. Edmund degradation was useful for sequencing smaller length proteins, such as proteins with about 40 or 50 amino acids. But for proteins which have a much longer length or large proteins, you would want to use mass spectrometry. So towards mass spectrometry, there were three very important steps. The first one was protein ionization, in which we studied MOLDI, ESI and soft ionization techniques, whereby you can insert a proton on top of a protein and charge it for further analysis. So once your protein is ionized, next it moves into the mass analysis chamber. So the mass is measured for the protein with the proton in the ionized state of course and later that protein is fragmented using tandem mass spectrometry and you measure the mass of the fragments as well. So the first step, the MS1, was simply the measurement of intact protein and intact protein mass. For the MS2, we measure the masses of the ions that are produced as a result of protein fragmentation. So using computational strategies, we estimated the protein mass and scored the whole protein mass and tried to compare it with the DB and find out those proteins in the protein databases such as Uniprot which match the mass of the intact protein. Next after protein fragmentation, we obtained the peptide masses and we computed the peptide sequence tags by looking at consecutive peaks within the spectrum. And lastly, we searched for post-translational modifications as well by looking at specific mass differences between the consecutive peaks. So once you have computed the entire spectrum and found the protein out, you would want to score and find out which protein from the Uniprot database matches with your spectrum the most. So the protein that is the closest to the protein that you are searching for is your protein. Now online tools for this entire activity are also available such as Mascot, ProcitePC and Sequest.