Strategies for Using MALDI-MS in Protein Biochemistry

Acylated peptides HCCA Ethyl acetate Liquid-liquid extraction 

Sulfated peptides DHAP Diammonium citrate Negative-ion mode 

If the dried-droplet method does not produce good results, then various other sample deposition techniques should be attempted, including various sandwich methods [2,18] and the fast evaporation method, also referred to as the thin-layer method [19]. 

Matrix mixtures have also been used for improved MALDI-MS performance for both proteins and peptides. For example, a mixture of DHB and HCCA was found to improve spot-to-spot reproducibility for peptide mass mapping and to increase the protein sequence coverage [20]. For examples of other matrices useful for peptide analysis, see Table 3.2. Membrane proteins can be efScientiy analyzed using optimized sample preparation methods and detergents, as described by Cadene and Chait [22]. Also, in situ liquid-liquid extraction using ethyl acetate and HCCA may enable the analysis of integral membrane proteins by MALDI-MS [23]. For additional information on the choice of matrix and sample preparation, see also Chapter 1, Section 1.8. 

Comparison of the experimental and calculated mass values will reveal discrepancies that might originate from natural processing of the protein, or from chemical artifacts. The theoretical molecular mass of a protein and the derived peptides is calculated from the amino acid sequence using computer tools. 

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Strategies for Using MALDI-MS in Protein Biochemistry 111 Table 3.2 Matrices and sample preparation methods for peptide analysis by MALDI-MS. 

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