Different impact of staining procedures using visible stains and fluorescent dyes for large-scale investigation of proteomes by MALDI-TOF mass spectrometry.
Replicate 2-D gels were stained with four visible or fluorescent dyes using published procedures, and 48 co-detected spots were selected for contrasting values in abundance, M(r) and pI. Success rate of identification and sequence coverage were affected in a dye-dependent manner by the three parameters. Frequency of missed cleavages and recovery of sulfur-containing peptides also depended on the dye. Finally, the dataset was used to predict the number of proteins identifiable when integrating the differential contribution of each parameter. Sypro Ruby appeared to combine several favorable features: no dependence of the identification rate upon the physicochemical properties of proteins, no impact on frequency of missed cleavages, and a higher predicted identification rate.
Chevalier
François
F
Laboratoire de Protéomique, INRA, UR 1199, 2 place Viala, 34060 Montpellier Cedex 1, France.
Centeno
Delphine
D
Rofidal
Valérie
V
Tauzin
Marc
M
Martin
Olivier
O
Sommerer
Nicolas
N
Rossignol
Michel
M
D029681:Arabidopsis Proteins / Q000032:analysis / Q000737:chemistry; D002478:Cells, Cultured; D015180:Electrophoresis, Gel, Two-Dimensional; D005456:Fluorescent Dyes; D020543:Proteome / Q000032:analysis / Q000737:chemistry*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013194:Staining and Labeling
D029681:Arabidopsis Proteins; D005456:Fluorescent Dyes; D020543:Proteome