Dinoflagellates are notorious for their ability to form the harmful algal blooms known as “red tides,” yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation. Not only is the transcriptomic response of dinoflagellates to environmental change generally muted, but there is a markedly low degree of congruency between mRNA expression and protein expression in dinoflagellates. Herein we discuss the application of high-throughput proteomics to the study of dinoflagellate biology. By profiling the cellular protein complement (the proteome) instead of mRNA (the transcriptome), the biomolecular events that underlie the changes of phenotypes can be more readily evaluated, as proteins directly determine the structure and the function of the cell. Recent advances in proteomics have seen this technique become a high-throughput method that is now able to provide a perspective different from the more commonly employed nucleic acid sequencing. We suggest that the time is ripe to exploit these new technologies in addressing the many mysteries of dinoflagellate biology, such as how the symbiotic dinoflagellate inhabiting reef corals acclimate to increases in temperature, as well as how harmful algal blooms are initiated at the sub-cellular level. Furthermore, as dinoflagellates are not the only eukaryotes that demonstrate muted transcriptional responses, the techniques addressed within this review are amenable to a wide array of organisms.

鞭毛藻以其形成有害藻华的能力而臭名昭著，这些藻华被称为“赤潮”，但对于藻华形成的机理仍知之甚少。尽管最近在核酸测序方面取得了进展，已经从暴露于各种不同条件的多种物种中产生了转录组，但测量RNA水平的变化通常并未深入了解鞭毛藻的细胞生物学或环境生理学，我们也没有深入了解支撑水华形成的分子事件。不仅鞭毛对环境变化的转录组反应通常被减弱，而且鞭毛的mRNA表达与蛋白质表达之间的一致性明显降低。在这里，我们讨论了高通量蛋白质组学在鞭毛藻生物学研究中的应用。通过分析细胞蛋白补体（蛋白质组）而不是mRNA（转录组），可以更容易地评估构成表型变化的生物分子事件，因为蛋白质直接决定细胞的结构和功能。蛋白质组学的最新进展已使该技术成为一种高通量方法，该方法现在可以提供与更常用的核酸测序不同的观点。我们建议，利用这些新技术来解决鞭毛藻生物学的许多谜团的时机已经成熟，例如，生活在珊瑚礁上的共鞭毛鞭毛藻如何适应温度的升高，以及在亚细胞水平上如何引发有害的藻华。此外，由于藻鞭毛不是唯一显示出静音转录反应的真核生物，因此本综述中涉及的技术适用于多种生物。