Detection of Proteins and Protein-Ligand Complexes Using HgTe Nanostructure Matrixes in Surface-Assisted Laser Desorption/Ionization Mass Spectrometry Cheng-Kang Chiang, † Zusing Yang, † Yang-Wei Lin, † Wen-Tsen Chen, † Han-Jia Lin, ‡ and Huan-Tsung Chang* ,† Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan, and Institute of Bioscience and Biotechnology, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, Taiwan We have analyzed peptides, proteins, and protein-drug complexes through surface-assisted laser desorption/ ionization mass spectrometry (SALDI-MS) using HgTe nanostructures as matrixes. We investigated the effects of several parameters, including the concentration of the HgTe nanostructures, the pH of the buffer, and the concentration of salt, on the performance of this system. When HgTe nanostructures are used as matrixes, [M + H] + ions were the dominant signals. Relative to other commonly used nanomaterials, HgTe nanostructures provided lower background signals from metal clus- ters, fewer fragment ions, less interference from alkali- adducted analyte ions, and a higher mass range (up to 150 000 Da). The present approach provides limits of detection for angiotensin I and bovine serum albu- min of 200 pM and 14 nM, respectively, with great reproducibility (RSD: <25%). We validated the ap- plicability of this method through the detections of (i) the recombinant proteins that were transformed in E. coli, (ii) the specific complex between bovine serum albumin and L-tryptophan, and (iii) a carbonic anhydrase-acetazolamide complex. Our results sug- gest that this novel and simple SALDI-MS approach using HgTe nanostructures as matrixes might open several new ways for proteomics and the analysis of drug-protein complexes. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a commonly used, powerful tool for the rapid quantification and identification of large biomolecules, including proteins, peptides, and nucleic acids. 1 Rapid energy transfer from UV-absorbing matrixes allows analytes to undergo soft and efficient desorption and ionization with minimal degrees of fragmentation. Unfortunately, inhomogeneous crystallization of analytes within organic matrixes commonly creates “sweet spots” during MALDI-MS analyses, with associated problems of low accuracy and poor shot-to-shot and sample-to-sample reproduc- ibility. 2 Detection of noncovalent complexes is difficult when MALDI- MS is used, primarily because the classic matrixes [e.g., sinapinic acid (SA)], typical additives (e.g., trifluoroacetic acid), and commonly used organic solvents (e.g., acetonitrile) tend to disrupt weakly bound complexes under laser irradiation. 3 Therefore, unlike electrospray ionization (ESI), MALDI is rarely used for the mass spectrometric detection of weak protein complexes. Only a few MALDI-MS approaches using less acidic matrixes, such as 6-aza-2-thiothymine (ATT), 4 2,4,6-trihydroxyacetophenone (THAP), 5 and 3-hydroxypicolinic acid (HPA), 4b,5c have been demonstrated for the detection of protein-protein, 4a,5a,b protein-DNA, 4b and protein-peptide 5c complexes. 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