Ideally, each MS2 spectrum would contain enough information to go back unambiguously to the sequence of its parent precursor. Since this is actually rarely the case, a strategy called Database Searching is usually used instead. MS2 fragmentation spectra are used to identify the sequence behind their MS1 parent peak. However, MS2 spectra rarely allow unambiguous […]

Data Dependent Acquisition (DDA) is the standard method for running LC-MS/MS experiments. Here, we present a quick overview of the DDA method, as well as of the less common Data Independent methods (DIA). In LC-MS/MS, purified peptides are separated on an online chromatography gradient (usually low pH Reverse Phase) over 1 to 4h and progressively […]