Comparison of SYPRO Ruby and Deep Purple using commonly available UV transilluminator: wide-scale application in proteomic research.
Fluorescent stains are becoming increasingly useful in proteomics research involving protein expression as well as post-translational modification studies and are particularly useful for samples which are expensive and scarce. The fluorescent dyes Deep Purple and SYPRO Ruby are widely used in protein expression studies. Using UV transillumination and Charged Coupled Device (CCD) based imaging system, their relative sensitivity to detect proteins separated by two-dimensional polyacrylamide gel electrophoresis and downstream protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was compared. Using mouse liver homogenate, we detected a greater number of spots using SYPRO Ruby over Deep Purple stain. However, the number of matched peptides and the percentage of amino acid residues identified for 21 different proteins were comparable suggesting their equivalency for LC-MS/MS identification. In spite of comparable MS compatibility, we recommend the use of SYPRO Ruby for expression proteomics due to its higher sensitivity in detecting protein spots.
Keck Graduate Institute of Applied Life Science, 535 Watson Drive, Claremont, California 91711, USA. bulbul_chakravarti@kgi.edu
Bulbul
B
Chakravarti
Wongrat
W
Ratanaprayul
Neville
N
Dalal
Deb N
DN
Chakravarti
D000818:Animals; D002853:Chromatography, Liquid; D015180:Electrophoresis, Gel, Two-Dimensional; D005456:Fluorescent Dyes; D008099:Liver / Q000737:chemistry; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D009942:Organometallic Compounds; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D012680:Sensitivity and Specificity; D053719:Tandem Mass Spectrometry; D014466:Ultraviolet Rays
D005456:Fluorescent Dyes; D009942:Organometallic Compounds; D020543:Proteome; C515601:Sypro Ruby