Quantitative evaluation of sample application methods for semipreparative separations of basic proteins by two-dimensional gel electrophoresis.
The use of cup-loading for sample application has become widely used in two-dimensional electrophoresis (2-DE) for resolution of basic proteins, but no side-by-side quantitative study has been published which compares cup-loading with the alternative passive and active rehydration methods to fully promote one type of loading method over another. Replicate 2-D gels from each loading method were quantitatively evaluated for gel-to-gel reproducibility using IPG 6-11 strips and semipreparative protein loads (300 microg). Gels were stained with SYPRO Ruby and analyzed with PDQuest. An inexpensive home-made assembly for cup-loading was used with the Protean IEF Cell for separation of whole cell extracts from the archaeon, Sulfolobus solfataricus. Cup-loading was determined to be far superior for IPG 6-11 separations than active or passive rehydration methods. Cup-loading consistently produced the greatest number of detectable spots, the best spot matching efficiency (56%), lowest spot quantity variations (28% coefficient of variation, CV), and the best-looking gels qualitatively. The least satisfactory results were obtained with active rehydration, followed closely by passive rehydration in off-line tubes. Passive rehydration experiments, performed using an on-line isoelectric focusing (IEF) tray, produced comparable spot numbers to cup-loading (84%), with 55% of the spots having higher intensity but 10% more spot quantity variance than cup-loading.
Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
Richard C
RC
Barry
Britt L
BL
Alsaker
James F
JF
Robison-Cox
Edward A
EA
Dratz
D024361:Amino Acids, Basic; D001426:Bacterial Proteins / Q000302:isolation & purification*; D015180:Electrophoresis, Gel, Two-Dimensional / Q000295:instrumentation* / Q000379:methods / Q000592:standards; D040901:Proteomics / Q000295:instrumentation / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D055672:Static Electricity; D016944:Sulfolobus / Q000737:chemistry
D024361:Amino Acids, Basic; D001426:Bacterial Proteins