Orbitrap LC-MS/MS Data Acquisition Method to Increase the Depth of Analysis for Low Amounts of Proteins in Complex Protein Mixtures

摘要

We have shown that excluding peptides analyzed in a control sample can increase the depth of analysis for a tagged protein sample. In many protein-protein interaction studies, some of the interacting proteins are present in very low amounts. To make the analysis even more challenging, these low abundance proteins are often present in highly complex mixtures with abundant contaminants. Thus, it can be extraordinarily difficult to comprehensively analyze the proteins of interest.