In recent study of proteomics, mass spectrometry(MS) is an essential tool for rapid and high sensitivity protein analysis. To perform high quality analysis, it is important to understand the characteristics of various MS analyzers, because different combination of ionization procedure and MS detector shows different performances in terms of ionization efficiency, peak resolution and data acquisition efficiency depended on scan speed. Here we evaluated the characteristics of ESI-IT MS(LCQ, Thermo Electron), ESI-QTOF MS(QSTAR, Applied Biosystems), and MALDI-TOFTOF MS(4700, Applied Biosystems). For the preparation of test samples, soluble fraction of HCT116 cells were separated by SDS-PAGE, and visualized by negative staining. Some protein bands were excised, digested by trypsin, and the peptides were recovered for MS analysis. In case of ESI-IT and ESI-QTOF, peptide solution was injected to reversed phase LC-MS system while the solution was crystallized with alpha-cyano-4-hydroxycinnamic acid for MALDI-TOFTOF. The database searching for protein identification was performed with Mascot(Matrix Science). When we focused on a unique protein obtained from a selected band, number of assigned MSMS spectra detected from ESI-IT, ESI-QTOF and MALDI-TOFTOF, were 34, 34, 3 respectively. The efficiency of MSMS analysis with MALDI-TOFTOF was very low in comparison with ESI-IT and ESI-QTOF. However, when we consider peptide mass fingerprinting method in MALDI-TOFTOF, 52 peptide peaks were assigned and sequence coverage was increased. The overlaping of assigned peptides among three instruments were low, because the molecular weight distribution of the peptides were different, for example, the average value of the molecular weight of parent ions obtained from ESI-QTOF, ESI-IT and MALDI-TOFTOF were 1280, 1860, 2040Da respectively. In the poster, we will show more data to understand the difference of the characteristics, and discuss how to show the best performance of those instruments.
