Because of the necessary of the diverse crucial biological role of both free and conjugates carbohydrates there is an important need for glyco sequencing. In biochemical protein analysis, the glyco part is usually cleaved off the protein and isolated by chromatographic means. Identification and structural elucidation can be performed by NMR, digestion by exoglycosidases and comparison to standard retention times. However, each of these methods has distinct drawbacks such as large sample amounts needed and also a limited number of standard structures. Therefore, methods which use very little sample and yield general sequence information are needed. Mass spectrometry, by producing the molecular weight and structural information in terms of hexoses, N-acetyl hexoses, sialic acids and pentoses, can can be used to identify the carbohydrate.
Similarly, routine and sensitive techniques exist for the sequencing of nucleotides. However, by their nature these methods are intrinsically limited to the analysis of samples composed of the known units (A,C,G,U,T). In contrast, mass spectrometry is a general detection method for all variants of the basic units of the oligonucleotides. Structural elucidation based on MALDI MS/MS spectra of a modified nucleotide is presented MALDI metastable decay has recently been introduced by Kaufmann and Spengler for the sequencing of peptides [1]. Carbohydrates can be analyzed in a way similar to peptides with this method. Results for the analysis and detection of relatively large carbohydrates with sialic acids (above 1.5 kDa), followed by the sequencing of the same carbohydrates are presented. For nucleotides best results were obtained when the samples were applied to the target in 3-hydroxypicolinic acid dissolved in 5 mM ammonium-tartrate. This sample preparation method leads to ions with less internal energy and less fragmentation and, thus, stable ions can be obtained in positive mode. Fragmentation of the molecular ion was performed as for peptides.
Metastable ions of all types of carbohydrates and small oligonucleotides investigated so far could be correlated with their sequence.