An improved detergent-compatible gel-fractionation LC-LTQ-Orbitrap-MS workflow for plant and microbial proteomics

In proteomics, liquid chromatography coupled to mass spectrometry (LC-MS/MS) is an invaluable technique to accurately identify and quantify large sets of proteins. In this chapter we show a time-effective, and detergent compatible, Ge-LC-LTQ-Orbitrap/MS proteomics workflow. The compatibility of this protocol with high concentrations of detergents significantly increases the extraction yield and the abundance of membrane proteins while gel fractionation increases the number of protein identifications. In our hands this workflow allows the identification of more than 1,500 proteins per sample, harvesting less than 20 mg of fresh weight, in many different organisms such as Chlamydomonas, Cyanothece, Arabidopsis, or Nicotiana, various microbes and enriched microbial samples.