Quantitation and LC-MALDI MS

Relative protein quantitation is the basis of all types of differential proteome analyses. In the 2D-gel approach protein staining with either visible or fluorescent dyes provides a reliable and sensitive method to detect changes in protein expression or isoform abundance. In the multidimensional LC approach quantitation relies mostly on stable isotope labeling and ratios between light and heavy isotopomers are determined by MS or MS/MS at the peptide level. Labeling can be performed on the protein level by 

For non-quantitative LC-MALDI applications, derivatization chemistry is not restricted to compounds which allow a convenient incorporation of heavy isotopes. For example for improved MS/MS detection sensitivity, tryptic peptides were labeled with sulfonated coumarin-tags at the N-termini after guanidylation of lysines (Pashkova et al. 2005). Despite reduced MS sensitivity for arginine-terminated peptides (in alpha cyano-4-hydroxycinnamic acid matrix), formation of y-ions was enhanced in MS/MS by the second mobile proton provided from the sulfonic acid group. For a SCX fraction from a E.coli hydrolysate 50% more peptides and 30% more proteins could be identified by multiplexed LC-MALDI MS and MS/MS after derivatization. 

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