Quantitation of Proteins by MALDI-MS

The relative quantitation of peptides is typically achieved by using stable isotope-labeled peptide analogs. For this, H-, C-, N- or 0-encoded peptides are frequently used [63]. Typical applications include the comparative analysis of proteins from healthy versus diseased cells, samples before and after treatmenL or cells in different states of metabolism. In each of such cases the mixture analysis will 

The in-vivo metaboHc labehng of proteins is achieved by growing cells in the presence of N-precursors [65, 66], or by the addition of isotope-labeled amino acids to the medium. The latter method is known as Stable Isotope Labehng by Amino Acids in CeU Culture (SILAC) [67, 68], and it provides the means for comparative analysis of protein abundance and post-translational modifications by MALDI-MS [69]. Commercially available alkylating reagents include ICAT (Cys) 

Label-free quantification can also be performed using MALDI-MS and MS/MS. 

One such method is based on ion intensities, assuming that there is a direct correlation between protein abundance and the area under the curve of the precursor ion spectra [75]. The other method is based on spectral counting, assuming a direct correlation between protein abundance and the number of MS/MS spectra obtained for the protein [76]. 

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