LC-MALDI increases the number of proteins identified
Application data
LC-MALDI-MS analysis of a 1D gel electrophoresis band is proven to offer a number of significant advantages over the conventional peptide mass fingerprinting approach widely used in proteomics:
Increase in information rich data
Improvement in proteome coverage of complex protein mixtures
Improved confidence level in protein match with greater probability scores being achieved.
LC-MALDI-MS target can be saved as a library of the gel digest where sample can be re-analysed in the future if required
Reduced number of peptides in each MALDI spot leads to fewer ion suppression effects
Results
MALDI alone. As a result of the complexity of the PMF spectrum and also suppression effects on ionisation caused by the large number of peptides
present in the mixture, only two proteins could be unequivocally identified: Phosphoglycerate kinase and Enolase
LC-MALDI. In contrast, 109 peptide candidates from the LC-MALDI-TOF run were analysed by MS/MS. Fragment ion mass lists were compiled for each of
these and assembled into a master mass list for MASCOT MS/MS ion search. 22 protein matches from the NCBInr database were found with ion scores
indicating identity or significant homology.
