Comparison of Performance of Matrix-Assisted Laser Desorption/Ionization-Time of Flight-Time of Flight and Electrospray Ionization-Quadrupole-Time of Flight for Qualification and Quantification of Proteins

To compare the performance of MALDI-TOF-TOF and ESI-Q-TOF in protein qualification and quantification,isobaric tags for relative and absolute quantification(iTRAQ) labeled peptides derived from trypsin-digested proteins in MCF7 cells with or without estrogen treatment were identified and quantified using MALDI-TOF-TOF and ESI-Q-TOF respectively.The experimental result showed that 1086 and 848 proteins were identified by MALDI-TOF-TOF and ESI-Q-TOF respectively,wherein 633 proteins were homolog;38 and 33 proteins were found to be differentially expressed by more than 0.5 fold by MALDI-TOF-TOF and ESI-Q-TOF respectively,wherein 3 proteins were the same proteins.The experimental data indicate that these two kinds of instruments were complementary both in peptide identification and relative quantification.Paralleled use of MALDI-TOF-TOF and ESI-Q-TOF significantly increased both the coverage and the confidence level of identified and quantified proteins.