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J Biomol Tech. 2010 September; 21(3 Suppl): S37.
PMCID: PMC2918199

Evaluation of the New MALDI Matrix 4-Chloro-Alpha-Cyanocinnamic Acid

M.E. Openshaw2
1University of Massachusetts Medical School, Shrewsbury, MA, United States;
2Shimadzu Biotech, Manchester, United Kingdom



Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF) continues to be an important tool for many proteomic studies. Recently Jaskolla, introduced a new rationally designed matrix (4 chloro-alpha-cyanocinnamic acid) which is reported to have superior performance as compared to the “gold standard” alpha-cyano-4-hydroxycinnamic acid. We decided to investigate the performance of this new matrix in the Shimadzu Biotech Axima TOF2. In this study we compared the performance of this new matrix to alpha-cyano-4-hydroxycinnamic acid in the analysis of protein digests. We looked at the overall sequence coverage as well as sensitivity in this comparison with standard protein tryptic digests. We also looked at the performance of this matrix with labile peptides such as phosphopeptides and 4-sulphophenyl isothiocynate derivitzed peptides (SPITC) to facilitate de novo sequencing. This matrix was found to be better performing than alpha cyano-4-hydroxycinnamic acid in overall sequence coverage since it has less of bias for C-terminal arginine containing peptides. It also showed as much as a 5 fold improvement in sensitivity with standard stainless steel targets. In addition due to the much cooler nature of this matrix labile peptides are readily seen intact with much less fragmentation in MS mode. This matrix was also evaluated in the MS/MS fragmentation modes of both post-source-decay (PSD) and collisional induced dissociation (CID). It was found that fragmentation occurs readily in CID however due the very cool nature of this new matrix the PSD fragments are quite weak. This matrix promises to be an important addition to the already extensive array of MALDI matrices once a good commercial source of a highly purified preparation becomes available. Jaskolla, T.W.; Lehmann, W.; and Karas, M. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 12200-12205.

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