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Buffers and detergents are notorious for suppression of analyte signal in electrospray and MALDI mass spectrometry and, invariably, analysts will take steps to remove these contaminants before MS analysis. However, we have found serendipitously that protein signal with MALDI MS is improved by about an order of magnitude on the addition of small amounts of Tween80. Four charged states of BSA could easily be seen at less than 125 fmol/spot and with mixture of three proteins (BSA, trypsinogen, and protein A) the molecular ions could be detected on as little as 12.5 fmol of spotted material (per protein) using an automated laser firing sequence.

The recent development of novel fragmentation processes based on either electron capture directly or transfer from an anion show great potential for solving problems in proteomics that are intractable by the more widely employed thermal-based fragmentation processes such as collision induced dissociation. The dominant fragmentation occurring upon electron capture dissociation of peptides is cleavage of N-C alpha bonds in the peptide backbone to form c and z* ions. In the case of disulfide-linked peptides, it has also been shown that electron capture on one of the cystine sulfur atoms is favored, resulting in cleavage of the disulfide bond. In this study, we report that electron capture on the sulfur of alkylated cysteine residues is also a dominant process, causing cysteine side-chain loss from z* ions.