Quantum dot enhancement of peptide detection by matrix-assisted laser desorption/ionization mass spectrometry.

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 heterogeneous 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 microscope. 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.

Magnetic iron oxide nanoparticle enrichment of phosphopeptides on a radiate microstructure MALDI chip.

Several methods can be used to improve the enrichment of phosphorylated proteins. In this paper, phosphopeptides were enriched using magnetic iron(II,III) oxide (magnetite, Fe(3)O(4)) nanoparticles (NPs) on a radiate microstructure silicon chip and then analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) without further purification processes. We have developed a radiate microstructure chip on which samples can be concentrated for analysis by MALDI-TOFMS. The phosphoprotein digests and magnetic iron oxide NPs aqueous solution were deposited onto the central zone of the radiate microstructure silicon chip and enabled the on-chip enrichment of phosphopeptides. Microscopic analysis confirmed that the applied samples were confined to the central zone. Sample spots focused on the chip were much smaller than those on an unmodified plate with the same total volume. Different additives were used and optimized processes were performed to minimize non-phosphopeptides interference. These data collectively demonstrate that our on-chip phosphopeptide enrichment protocol is a rapid and easy-to-use method for phosphoproteome analysis.

A radiate microstructure MALDI chip for sample concentration and detection.

Although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis is an important tool for analyzing and characterizing biomolecules of varying complexity, the sensitivity of MALDI-TOFMS is dependent on proper preparation of the sample, a process that is oftentimes problematic and requires considerable expertise. In this study, we have developed a radiate microstructure chip on which samples can be concentrated for analysis by MALDI-TOFMS. The sample/matrix mixture was deposited onto the central space of the well on the chip and allowed to dry. Microscopic analysis confirmed that the applied samples were confined to the central zone. Sample spots focused on the chip were much smaller than those on an unmodified plate with the same total volume. Optimizing processes of several preparation factors were also performed to ensure matrix homogeneity in our chip. Analysis of the samples with MALDI-TOFMS showed that the signals from samples on our chip were significantly greater than those on the unmodified plate. The feasibility of using this chip to detect peptides and phosphopeptides was also demonstrated.