Detergents in Proteomics - benefits and pitfalls

Proteomics has made great advances toward achieving the aim of identifying, quantifying and analyzing the full repertoires of proteins in biological samples (the proteome). Yet there are proteins that are rarely detected due to extraction challenges.

In order to include in the proteomic analysis membranal proteins from different organelles of the cells, isolation and solubilization of membrane are needed and detergents are frequently used. In addition, gradual use in detergent can be beneficial for organelle separation and extraction and their presence may also have a major role on the protein profile.

Another frequent use of detergents is prevention of non-specific binding in affinity purification and immunoassay procedures.

Although they are extremely useful, detergents often cause ion suppression and high noise at the mass spectrometry analysis.

In this study we will present the benefits and the pitfalls of different detergents types and changes in the data due to the different extraction procedures. Moreover, we will present methods to eliminate detergents from the protein samples prior to the mass spectrometry analysis thus improving the data.