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LC-MALDI and MALDI-MS/MS for the Analysis of Complex Peptide Mixtures

roteins from the 50 protein mixture. Additionally, 4 other proteins were also identifi ed which were not intentionally supposed to be present in the sample. It is believed that the use of multiple (complementary) mass spectrometric techniques, e.g. electrospray LC-MS/MS, would result in the identifi cation of even more proteins. These results are very encouraging and demonstrate the potential of the LC-MALDI technique combined with MALDI-MS/MS for the analysis of protein mixtures.

iTRAQ Labelled Sample
Results obtained using a 5-protein test mix demonstrated that the AXIMA-TOF2 can be used for the relative quantifi cation of proteins using the iTRAQ labelling technology. Using the 114 and 117 reagents, the fragment ion resolution obtained in MS/MS mode is suffi cient to allow the determination of relative expression levels between samples with high precision (15%). For higher mass precursor ions, a novel MALDI-MS/MS analysis mode (LMZ) can be used to enhance the fragment ion resolution and sensitivity of the low mass fragment ion region containing the iTRAQ reporter ions. It should be stated that the LMZ mode is often not necessary for lower mass precursors as the fragment ion resolution obtained at lower mass in full MS/MS mode is suffi cient for the quantifi cation calculations.


Conclusions
LC-MALDI is a suitable technique for the automated analysis of complex protein mixtures.

When coupled with the AXIMA-TOF2 MALDI-TOF mass spectrometer, the high-energy MS/MS provides high confi dence identifi cations.

Relative quantifi cation can be achieved using the iTRAQ technology. A novel MS/MS mode (Low Mass Zoom) can be used, if required, to enhance the resolution and signal intensity of low mass fragment ions.



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