Published: July 18, 2011 r2011 American Chemical Society 6593 dx.doi.org/10.1021/ac201016c | Anal. Chem. 2011, 83, 6593–6600 ARTICLE pubs.acs.org/ac Quantum Dot Enhancement of Peptide Detection by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Chih-Wei Liu, † Min-Wei Chien, † Guo-Feng Chen, § Shun-Yuan Chen, †,‡ Chih-Sheng Yu, ‡ Ming-Yuan Liao,* ,§ and Chien-Chen Lai* ,†,^ † Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan ‡ Instrument Technology Research Center, National Applied Research Laboratories, Taiwan § Department of Chemistry, National Chung Hsing University, Taichung, Taiwan ^ Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan b S Supporting Information M atrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is an important analyti- cal tool for characterization of biomolecules. 1À8 In MALDI, conventional organic matrixes (e.g., R-cyano-4-hydroxycinnamic acid, CHCA) absorb the energy of the laser pulse and then transfer it to the surrounding analytes for desorption and ioniza- tion. However, the heterogeneous cocrystallization of analytes and organic matrixes often leads to the formation of invisible “sweet spots” that affect the shot-to-shot reproducibility during MALDI analysis. At the same time, detection of “sweet spots” is a time-consuming process. Another limitation of MALDI is or- ganic matrix interference in the low-mass region (m/z of <500), thereby making the technique unsuitable for the analysis of small molecules. Surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOFMS) overcomes the above-mentioned problems of MALDI. SALDI uses inorganic nanoparticles (NPs) as a matrix for desorption and ionization of analytes. 2,9 Organic matrixes and inorganic NPs play similar roles during the laser pulse. NPs have been widely employed in the qualitative and quantitative investigations of biomolecules. 2,9À21 Furthermore, NPs can act as selective probes for effective enrichment of ana- lytes because of the unique size-dependent chemical and physical properties of bare NPs and the functionalized capping ligands. Although the enrichment process can improve the sensitivity of detection, the process requires sufficient time for the analytes to react with the NPs. Studies have shown that fluorescent quantum dots (QDs) are useful materials in preparing samples for laser desorption/ ionization mass spectrometry (LDI-MS). 21À25 For example, Shrivas et al. demonstrated that the use of CdSe QDs as the matrix and the concentrating probes increased the detection sensitivity of peptides in SALDI-MS. 24 Bailes et al. found that the application of CdSe/ZnS QDs as comatrixes resulted in superior signal-to-noise ratios, markedly better peak quality, and the detection of more peptides in MALDI MS. 25 Moreover, Kailasa et al. reported that Mn 2+ -doped ZnS@cysteine NPs, which exhibit a high surface area-to-volume ratio and good photostability, are Received: April 20, 2011 Accepted: July 18, 2011 ABSTRACT: Matrix-assisted laser desorption/ionization time- of-flight mass spectrometry (MALDI-TOFMS) is a rapid and sensitive tool for characterizing a wide variety of biomolecules. However, invisible “sweet spots” that form during heteroge- neous cocrystallization minimize the analytical throughput and affect the reproducibility of MALDI analysis. In this study, visible “sweet spots” were generated on a metallic sample plate by quantum dots (QDs)-assisted MALDI analysis. To the best of our knowledge, this is the first report to demonstrate that “sweet spots” can be observed directly without using a micro- scope. The proper proportion of matrix to QDs that results in optimal crystallization was also examined. The signals of standard peptides and phosphopeptides obtained by QD-assisted MALDI analysis were 5- and 3-fold higher, respectively, than those obtained by conventional MALDI analysis. For peptide mixtures, the QD-assisted MALDI analysis not only resulted in more intense peptide signals but also resulted in a greater number of peaks, thereby allowing for better detection of individual peptides in peptide mixtures. Moreover, we demonstrated that application of QDs to a radiate microstructure chip followed by MALDI analysis enhanced the detection of peptide signals. Overall, we show that this method is a simple, sensitive, and high-throughput technique for peptide detection.