title: Comparison of SYPRO Ruby and Flamingo fluorescent stains for application in proteomic research.
abstract: Fluorescent dyes are widely used for the detection and quantitation of proteins separated by polyacrylamide gel electrophoresis. SYPRO Ruby is one such fluorescent dye widely used for this purpose. More recently, another fluorescent dye, Flamingo, is available for expression proteomic research. Using a standard ultraviolet (UV) transilluminator and a charge-coupled device (CCD)-based imaging system, the relative sensitivity of these two different fluorescent stains with regard to detection of protein spots separated by two-dimensional gel electrophoresis (2D-GE) and identification by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) were compared. Using mouse kidney and liver homogenates as well as Escherichia coli extract, we detected a greater number of protein spots using Flamingo compared with SYPRO Ruby. In addition, when we compared the number of matched peptides and the percentage of amino acid residues identified for 22 different protein spots of mouse kidney proteome, we observed a higher number of matched peptides and a higher percentage of amino acid residues for the majority of the proteins using Flamingo compared with SYPRO Ruby. Also, we were able to characterize a protein spot that can be detected by Flamingo only. Therefore, we recommend Flamingo over SYPRO Ruby to be used for studies on expression proteomics.
authors.affiliation: Keck Graduate Institute of Applied Life Sciences, Claremont, CA 91711, USA. bulbul.chakravarti@gmail.com
authors.forename: Bulbul
authors.initials: B
authors.lastname: Chakravarti
authors.forename: Pamela
authors.initials: P
authors.lastname: Fathy
authors.forename: Michael
authors.initials: M
authors.lastname: Sindicich
authors.forename: Buddhadeb
authors.initials: B
authors.lastname: Mallik
authors.forename: Deb N
authors.initials: DN
authors.lastname: Chakravarti
mesh_terms: D000818:Animals; D002851:Chromatography, High Pressure Liquid; D015180:Electrophoresis, Gel, Two-Dimensional; D005456:Fluorescent Dyes / Q000737:chemistry*; D007668:Kidney / Q000378:metabolism; D008099:Liver / Q000378:metabolism; D051379:Mice; D009942:Organometallic Compounds / Q000737:chemistry*; D011506:Proteins / Q000032:analysis* / Q000302:isolation & purification; D040901:Proteomics / Q000379:methods*; D021241:Spectrometry, Mass, Electrospray Ionization; D013194:Staining and Labeling; D014466:Ultraviolet Rays
chemical_list: D005456:Fluorescent Dyes; D009942:Organometallic Compounds; D011506:Proteins; C515601:Sypro Ruby