Introduction: Mass spectrometry has become an important tool for protein analysis and peptide sequence determination. Typically, a protein mixture is proteolytically digested, analyzed by mass spectrometry, and then searched against a relevant protein database where identification can be made by comparing experimental MS/MS peptide spectra with those predicted by theory. MALDI-based mass spectrometry methods are not suitable or complex sample analysis – before MALDI-MS, the sample is often separated by chromatography or electrophoresis. In this study, proteins from a yeast cell lysate were extracted by protein G beads and separated by one-dimensional SDS PAGE gel electrophoresis. Ten gel bands of interest were excised and digested. The resulting peptide fragments were analyzed using both MALDI-TOF and AP MALDI-ion trap. The MS results from MALDI-TOF were searched by Mascot software. Two proteins were identified. The MS/MS spectra from the AP MALDI-ion trap system were searched by TurboSEQUEST™ software. Ten proteins were identified. The ability to generate MS/MS spectra by coupling MALDI ionization with ion trap mass spectrometry provides higher confidence and greater accuracy for protein identification compared to MALDITOF mass fingerprinting.

Conclusions: Both MALDI-TOF and AP MALDI-ion trap are powerful tools for the identification of proteins from gel bands. MALDI-TOF offers a fast, easy method for peptide mass fingerprinting. AP MALDI-ion trap is also fast and easy to use. In addition, when used with TurboSEQUEST software, it utilizes the structural information included in MS/MS spectra of peptides as a basis for protein identification. This can be very helpful in analysis of mixtures and modified peptides which can create issues for MALDI-TOF. The creation of MS/MS spectra by the AP MALDI-ion trap system makes it extremely useful for the identification of proteins from gel spots or bands. It offers clear dvantages over MALDI TOF techniques.

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