Enrichment of serum amyloid proteins by hydrophobic interaction chromatography combined with two-dimensional electrophoresis with immobilised pH gradients

Large-scale identification of cytosolic mouse brain proteins by chromatographic prefractionation

Proteomic studies on mouse brain protein expression are still holding center stage as the generation of a reference database for the brain proteome, a need for designing expressional studies at the protein level. We therefore decided to extend the amount of identified brain proteins by the use of prefractionation. In order to reduce the complexity of mouse brain proteome we applied chromatographic prefractionations, ion-exchange and hydrophobic interaction chromatography, prior to 2-DE, followed by mass spectrometric identification (2-DE MALDI-MS). We analyzed about 17,000 protein spots in cytosolic fractions of mouse brain and identified about 10,000 spots. A total of 1841 proteins showing different pI or M(r), representing probably post-translational modifications or splice variants, were products of 789 different genes. Numerous proteins were clearly identified as metabolic, antioxidant, cytoskeleton, signaling, transcription/translation, nucleic acid-binding, proteolysis-related proteins. We additionally provided evidence for the existence of hypothetical proteins predicted from nucleic acid sequences. Moreover, observed pIs of proteins are listed thus enabling localization of proteins in a gel, information that cannot be obtained from theoretical pI's in databases. The results represent so far the largest database of mouse brain proteins and provide valuable information for the design of proteomic studies in the mouse.

Purification and separation of hydrophobic serum amyloid A precursor isoforms by a one-step preparative method

The levels of two major serum amyloid A precursor isoforms, SAA1 and SAA2, which are associated with high-density lipoproteins (HDL) are increased during inflammation. The hydrophobic character and the small size difference--corresponding to just 0.8 kDa--between these two members of the SAA family hinder their separation and purification on a large scale by conventional methods. In the current work, both mouse SAA proteins were purified from HDL-SAA and acute-phase serum within 10 h in a one-step procedure using the high-resolution, continuous-elution preparative gel electrophoresis Prep-Cell system in combination with Tris/Glycine SDS-PAGE. Moreover, applying the Tris/Tricine system on the Prep-Cell resulted not only in purification of the SAA proteins, but also in their separation within 16 h. The SAA isoforms were freed from SDS using a Centricon concentrator and were identified using monoclonal antibodies. Optical density profile plots of gel protein or Western blot bands in combination with a colorimetric spectrophotometric protein assay showed that the recovery of the isoforms ranged from 38% to 60%. These results show that the preparative gel electrophoresis system Prep-Cell is a suitable device for separating SAA1 and SAA2 proteins in a simplified, convenient, and fast procedure, which can be applied on a small or large scale.