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It is a strong organic base that exists primarily as guanidium ions at physiological pH. It is spontaneously already present in urine. It is also used as a protein denaturant in laboratory research. It is also used in the treatment of myasthenia and as a fluorescent probe in HPLC.
Protein digestion is an integral part of the “shotgun” proteomics approach and often requires overnight incubation prior to mass spectrometry analysis. A quadruplicate “shotgun” proteomics analysis of whole yeast lysate showed that Guanidine-Hydrochloride (Gnd-HCl) protein digestion could be optimally completed within 30 min by the endoprotease Lys-C. No chemical structures appear when samples are incubated in Gnd-HCl at 95 °C, making Gnd-HCl a suitable digestion buffer for shotgun proteomics. Current methodologies for investigating protein-protein interactions (PPIs) often require several preparatory steps that prolong any parallel processing and high-throughput interaction analysis. Gnd-HCl allows efficient elution and subsequent rapid digestion of PPIs to provide a high-throughput methodology suitable for proximity-purification mass spectrometry (AP-MS) experiments. To validate the Gnd-HCl approach, label-free PPI analysis of several GFP-tagged yeast dewatering enzymes was performed. The identification of known interaction partners demonstrates the utility of the optimized Gnd-HCl protocol, which is also scalable to 96-well plate format.