We report a novel method termed matrix suppressed laser desorption/ionization to improve the analysis of low-mass molecules by MALDI-TOF mass spectrometry. In this method, the surfactant of cetrimonium bromide (CTAB) is added to the conventional matrix of r-cyano-4-hydroxycinnamic acid solution to prepare the MALDI samples. During the MALDI process, the presence of CTAB could substantially or even completely suppress the matrixrelated ion background. As a result, very clean mass spectra can be routinely obtained in the low-mass range. In addition, the presence of CTAB can significantly improve the mass resolution of low-mass molecules. It is seen that high-quality spectra were routinely obtained at a matrix/CTAB ratio of 1000:1. This method has been successfully used to analyze a variety of low-mass molecules.Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has become a very powerful tool to analyze large synthetic polymers and biomolecules. 1 However, it has been a challenge to use MALDI for the analysis of low-mass analytes (m/z <500 Da). This challenge is due in part to the presence of a variety of abundant matrix-related ions in the low-mass range of spectra, because most of the currently used matrixes have molecular weights less than 300, and during laser irradiation, they also act as their own matrixes, producing a variety of matrix-related ions. This can also limit the utility of MALDI-TOF in several important applications, including the automated, high-throughput combinatorial and chip-array analysis.Considerable efforts have been made and several alternative approaches have been developed to overcome this problem. The first is a matrix-free approach in which the sample substrate acts as matrix. 2-5 For example, Buriak et al. 2 reported successful laser desorption/ionization on porous silicon (DIOS). Surface-enhanced neat desorption (SEND) introduced by Hutchens and Yip 5 is another matrix-free method for small molecule analysis.The second approach utilizes high-mass matrix molecules. 6,7 Ayorinde et al. 6 studied the use of high-mass porphyrin derivatives to replace conventional low-mass molecules such as R-cyano-4-hydroxycinnamic acid (CHCA) as the MALDI matrixes. They successfully demonstrated the use of mesotetrakis(pentafluorophenyl)porphyrin (F20TPP, MW 974.57) as a matrix for the MALDI-TOF analysis of low-mass surfactants. With F20TPP as the matrix, the fatty acids of saponified vegetable oils were also successfully analyzed. 7 The third approach uses inorganic compounds instead of organic molecules as matrix. 8-16 In 1988, Tanaka et al. 8 first reported the use of ultrafine metal powder in protein analysis. Since then, many inorganic materials, including graphite particles, 9-12 fine metal or metal oxide powder, 13 silver thin-film substrates or particles, 14 and silica gel, 15 have been used in the MALDI-TOF analysis of low-mass molecules. Schurengberg et al. 16 systematically investigated the particle suspensions, which include different particle materials, particl...

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Recent advances in genomics and proteomics have enabled the discovery of more drug targets than ever before. The majority of these drug targets are proteins. One of the most challenging areas of drug development is the search for novel receptor ± ligand pairs and enzyme inhibitors, [1,2] as many novel proteins have no known binding partners. During the drug discovery process, the binding partners of a receptor or protein must be found in order to determine possible ways to address its pathological pathway.Ligand fishing is a widely used process in which proteins are screened against a multitude of compounds to search for the binding partners of the proteins. The most common methods for ligand fishing are those based on direct binding and one of the most versatile direct-binding assays involves the use of biosensors based on surface plasma resonance (SPR). [3±5] However, a major drawback of SPR is that once a sample is identified as having a possible binding partner, other conventional biochemical techniques, for example, HPLC and mass spectrometry, [6] need to be applied to identify the new ligand.Herein we describe a novel on-probe direct-binding assay to screen the binding partners of a target protein. Contrary to the case in SPR, the captured binding partners in this directbinding assay are directly analyzed on-probe by means of mass spectrometry. The target protein is first immobilized on a porous silicon probe. A sample that contains possible binding partners is then incubated with the probe, and the binding partners are captured by the immobilized protein.The captured binding partner is then identified by means of on-probe laser desorption/ionization time-of-flight (TOF) mass spectrometric analysis.Unlike other mass spectrometry based assays in which biologically active probes are used for rapid analyses of a sample, [7±12] this new assay involves desorption/ionization on silicon (DIOS) [13±15] instead of matrix-assisted laser desorption/ionization (MALDI) in the ionization process. The use of DIOS is based on two considerations. First, the majority of the drug candidates are low-mass molecules. In MALDI, the matrix is essential to desorption/ionization, but the use of matrix also generates strong matrix-related background noise in the low-mass region, which obscures or even suppresses the analytical signals of other low-mass molecules. In contrast, a matrix is not required for DIOS and laser desorption/ ionization is performed on porous silicon, therefore eliminating the matrix-related background problem. DIOS is very effective for analysis of low-mass molecules. Second, DIOS involves the use of porous silicon as a probe on which proteins can easily be immobilized. Furthermore, the porous silicon probe can be generated routinely through electrochemical anodization [15,16] or chemical etching [17±19] of flat crystalline silicon. The porous silicon surface can be regenerated easily.A silicon wafer was galvanostatically etched and oxidized. The preparation of a good porous silicon probe is essential for ...

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