Peptide sequencing stable isotope labeling

D.R. Goodlett, A. Keller, J.D. Watts, R. Newitt, E.C. Yi, S. Purvine, J.K. Eng, P. von Haller, R. Aebersold, E. Kolker, Differential stable isotope labeling of peptides for quantitation and de novo sequence derivatization. Rapid Commun. Mass Spectrom., 15 (2001) 1214. 

Immunoenrichment can be applied at the peptide level, particularly in the stable isotope standards and capture by anti-peptide antibodies (SISCAPA) method (140). Target peptides together with their stable isotope-labeled counterparts (used as quantitation references) are enriched by antibodies that are developed against antigens with almost the same sequences. The antibodies are often covalently attached to magnetic beads for sample cleanup. This technique boasts an improved limit of quantitation and increased inter-laboratory reproducibility (141). 

The above facts do not favour protein or peptide quantitation using MALDI-MS. Some problems are associated with MALDI-MS quantification i) low shot-to-shot reproducibility, ii) various signal suppression effects, and iii) strong influence of sample preparation and matrix crystallisation. Nevertheless, it is possible to use MALDI-MS to obtain absolute or relative quantitation. In most cases, the idea is to use an internal standard for an absolute quantitation, but this standard must have the same physico-chemical characteristics as the quantified peptide. The use of a different peptide in terms of sequence may result in different desorption and ionisation properties. Usually, the internal standard is the same peptide labelled with a stable isotope to modify slightly the mass. 

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