Evaluation of the new MALDI matrix 4-chloro-alpha-cyanocinnamic acid.

MALDI-TOF continues to be an important tool for many proteomic studies. Recently, a new rationally designed matrix 4-chloro-alpha-cyanocinnamic acid was introduced, which is reported to have superior performance as compared with the "gold standard" alpha-cyano-4-hydroxycinnamic acid (CHCA). In this study, the performance of this new matrix, using the Shimadzu Biotech Axima TOF(2) (Shimadzu Biotech, Manchester, UK), was investigated. The overall sequence coverage as well as sensitivity of this matrix were compared with CHCA using standard protein tryptic digests. The performance of this matrix with labile peptides, such as phosphopeptides and 4-sulfophenyl isothiocynate-derivatized peptides, to facilitate de novo sequencing was also explored. This matrix was found to be better performing than CHCA in overall sensitivity and showed better sequence coverage at low-digest levels, partly as a result of less of a bias for arginine-containing peptides. It also showed as much as a tenfold improvement in sensitivity with labile peptides on standard stainless-steel targets. In addition, as a result of the much cooler nature of this matrix, labile peptides are readily seen intact with much less fragmentation in mass spectrometry (MS) mode. This matrix was also evaluated in the MS/MS fragmentation modes of post-source decay (PSD) and collisional-induced dissociation (CID). It was found that fragmentation occurs readily in CID, however as a result of the very cool nature of this new matrix, the PSD fragments were quite weak. This matrix promises to be an important addition to the already extensive array of MALDI matrices.