Visualization of mitochondria with cyanine dyes has been exploited to study the functions of mitochondria. However, proteins interacting with cyanine dyes have not been investigated clearly. Here, we report a chemical proteomics approach for the identification of mitochondrial proteins associated with cyanine dyes. This approach uses affinity-based photocrosslinking of Cy5-diazirine-alkyne (Cy5-DAyne) in combination with selective enrichment of target proteins by bio-orthogonal supramolecular latching based on unique host-guest interaction between cucurbit[7]uril (CB[7]) and its selected guest such as adamantylammonium (AdA). The enriched proteins then were analyzed using LC–MS/MS to provide a list of proteins closely associated with the Cy5 motif. This study suggests that the proteomic environment around the Cy5 motif is highly associated with energy production processes, including the respiratory chain, ATP synthesis, and fatty acid oxidization. Moreover, it demonstrates the potential of this chemical proteomic approach for the investigation of other organellar proteins using different selective dyes.

线粒体与花青染料的可视化已被用于研究线粒体的功能。然而，与花青染料相互作用的蛋白质尚未得到明确研究。在这里，我们报告了一种化学蛋白质组学方法，用于鉴定与花青染料相关的线粒体蛋白。这种方法使用基于亲和力的 Cy5-diazirine-alkyne (Cy5-DAyne) 光交联，结合基于葫芦[7]uril (CB[7]之间独特的主客体相互作用的生物正交超分子闭锁选择性富集目标蛋白) 及其选定的客体，如金刚烷基铵 (AdA)。然后使用 LC-MS/MS 分析富集的蛋白质，以提供与 Cy5 基序密切相关的蛋白质列表。这项研究表明，Cy5 基序周围的蛋白质组学环境与能量产生过程高度相关，包括呼吸链、ATP 合成和脂肪酸氧化。此外，它还展示了这种化学蛋白质组学方法在使用不同选择性染料研究其他细胞器蛋白质方面的潜力。