Protein identification with Teflon as matrix‐assisted laser desorption/ionization sample support

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Abstract
Protein identification is a critical step in proteomics, and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) plays an important role in that identification. Polytetrafluoroethylene (Teflon) was tested as a new MALDI sample support to improve protein identification. The tryptic peptides obtained from a model protein were bound to the surface of a modified MALDI sample holder via the hydrophobic interactions that occur between the Teflon surface and the peptide ion‐pairs, and the affinity of α‐cyano‐4‐hydroxycinnamic acid for the peptides. During that surface‐binding step, the peptide mixture was also desalted and concentrated. A greater number of matched peptides and a larger sequence coverage were obtained for the proteins when Teflon was used as the sample support compared with conventional sample preparation methods and a stainless‐steel surface. In addition, the characterization of a small amount of protein was improved with Teflon. Nine silver‐stained protein spots obtained from 2‐D gel of a human cerebrospinal fluid (CSF) proteome were identified by this method. Among the nine protein spots, peptide 6:c3c fragment and procollagen c‐proteinase enhancer were not annotated in any published 2‐D map of human CSF. A Teflon MALDI sample support is a low‐cost, simple, and effective method that can be used to improve the quality of the MALDI mass spectrum of a complex tryptic peptide mixture, and to achieve a higher level of reliability and success in protein identification. Copyright © 2002 John Wiley & Sons, Ltd.