title: Non-electrophoretic differential detergent fractionation proteomics using frozen whole organs.
abstract: Non-electrophoretic methods based on two-dimensional liquid chromatography followed directly by tandem mass spectrometry (2D-LC/MS(2)) have become the preferred method for high-throughput expression proteomics and are widely applied to fresh tissues. Pre-fractionation techniques are also used in combination with 2D-LC/MS(2) to both increase the proteome size and to assign cellular locations. Data from such experiments have become central to systems biology analyses. Here we apply a differential detergent (pre)fractionation (DDF) followed by 2D-LC/MS(2) to frozen archival tissues. Our results show that by using frozen archival tissues, we do not lose proteome coverage or the ability to assign proteins to cellular compartments. In addition, we were able to assign 'biological process' Gene Ontology (GO) annotations, which will facilitate systems biological modeling of our proteomics data.
authors.affiliation: College of Veterinary Medicine, PO Box 6100, Mississippi State University, MS 39762-6100, USA. bvandenberg@cvm.msstate.edu
authors.forename: Bart H J
authors.initials: BH
authors.lastname: van den Berg
authors.forename: Tya
authors.initials: T
authors.lastname: Harris
authors.forename: Fiona M
authors.initials: FM
authors.lastname: McCarthy
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Lamont
authors.forename: Shane C
authors.initials: SC
authors.lastname: Burgess
mesh_terms: D000818:Animals; D005591:Chemical Fractionation / Q000379:methods*; D002645:Chickens; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D015925:Cryopreservation / Q000379:methods; D003902:Detergents / Q000737:chemistry*; D004586:Electrophoresis; D009924:Organ Culture Techniques; D009926:Organ Preservation / Q000379:methods; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000032:analysis / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D013154:Spleen / Q000378:metabolism*
chemical_list: D003902:Detergents; D020543:Proteome