Now, we move onto the biological inference from the MS data. Identifying peptides from MS data is one of the popular tasks in MS data analysis. Nowadays, protein identification is regularly performed by tandem mass spectrometry (MS-MS). Because of the difficulty faced in measuring intact proteins using MS-MS, a protein is typically digested into peptides with enzymes and the MS-MS spectrum of each peptide is measured. Here, we present a recipe to identify peptides in MS data.
In this recipe, we will introduce a new R package named
protViz. The MS data we use in this recipe is artificially created from the previous data. The peptide we attempt to detect is the human serum albumin (ALB).