title: Using guanidine-hydrochloride for fast and efficient protein digestion and single-step affinity-purification mass spectrometry.
abstract: Protein digestion is an integral part of the "shotgun" proteomics approach and commonly requires overnight incubation prior to mass spectrometry analysis. Quadruplicate "shotgun" proteomic analysis of whole yeast lysate demonstrated that Guanidine-Hydrochloride (Gnd-HCl) protein digestion can be optimally completed within 30 min with endoprotease Lys-C. No chemical artifacts were introduced when samples were incubated in Gnd-HCl at 95 °C, making Gnd-HCl an appropriate digestion buffer for shotgun proteomics. Current methodologies for investigating protein-protein interactions (PPIs) often require several preparation steps, which prolongs any parallel operation and high-throughput interaction analysis. Gnd-HCl allow the efficient elution and subsequent fast digestion of PPIs to provide a convenient high-throughput methodology for affinity-purification mass spectrometry (AP-MS) experiments. To validate the Gnd-HCl approach, label-free PPI analysis of several GFP-tagged yeast deubiquitinating enzymes was performed. The identification of known interaction partners demonstrates the utility of the optimized Gnd-HCl protocol that is also scalable to the 96 well-plate format.
authors.affiliation: Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen.
authors.forename: Jon W
authors.initials: JW
authors.lastname: Poulsen
authors.forename: Christian T
authors.initials: CT
authors.lastname: Madsen
authors.forename: Clifford
authors.initials: C
authors.lastname: Young
authors.forename: Flemming M
authors.initials: FM
authors.lastname: Poulsen
authors.forename: Michael L
authors.initials: ML
authors.lastname: Nielsen
mesh_terms: D002846:Chromatography, Affinity / Q000379:methods*; D019791:Guanidine / Q000737:chemistry*; D057166:High-Throughput Screening Assays; D013058:Mass Spectrometry / Q000379:methods*; D008666:Metalloendopeptidases / Q000737:chemistry*; D025941:Protein Interaction Mapping / Q000379:methods; D059748:Proteolysis; D040901:Proteomics; D011993:Recombinant Fusion Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D014508:Urea / Q000737:chemistry
chemical_list: D011993:Recombinant Fusion Proteins; D029701:Saccharomyces cerevisiae Proteins; D014508:Urea; D008666:Metalloendopeptidases; C039830:peptidyl-Lys metalloendopeptidase; D019791:Guanidine