Mass Spectrometry

New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. The analysis of peptides generated by proteolytic digestion of proteins, known as bottom-up proteomics, serves as the basis for many of the protein research undertaken by mass spectrometry (MS) laboratories. Discovery-based or shotgun proteomics employs data-dependent acquisition (DDA). Herein, a hybrid mass spectrometer first performs a survey scan, from which the peptide ions with the intensity above a predefined threshold value, are stochastically selected, isolated and sequenced by product ion scanning. n targeted proteomics, selected environmental Monitoring (ERM), also known as multiple reaction monitoring (MRM), is used to monitor a number of selected precursor-fragment transitions of the targeted amino acids. The selection of the SRM transitions is normally calculated on the basis of the data acquired previously by product ion scanning, repository data in the public databases or based on a series of empirical rules predicting the Enzyme structure sites.