Surface-activated chemical ionization time-of-flight mass spectrometry and labeling-free approach: two powerful tools for the analysis of complex plant functional proteome profiles.

Surface-activated chemical ionization (SACI) has been widely used in recent years to analyze a range of different compounds (e.g., peptides, street drugs, amino acids). The main benefits of this technology are its high sensitivity and its effectiveness under different chromatographic conditions. Here, we used SACI in conjunction with a highly selective quadrupole time-of-flight mass analyzer to characterize a complex proteome pattern after separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The data obtained were compared with those obtained using the micro-electrospray ionization (ESI) approach, which showed that using SACI strongly increased the number of detectable proteins. The higher sensitivity is mainly due to the ability of SACI to selectively produce singly charged species of high intensity under full-scan conditions and doubly charged species for tandem mass spectrometric (MS/MS) peptide characterization by simply changing the ionization conditions during data acquisition.