Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, evidence is reviewed demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal proteins (RP) does not necessarily correspond to RP variability. Thus protein remodeling of ribosomes should be investigated by methods that allow direct quantification of RPs, ideally of isolated ribosomes. Such methods are reviewed, focusing on mass spectrometry and emphasizing method‐specific biases and approaches to control these biases. It is argued that using multiple complementary methods can help reduce the danger of interpreting reproducible systematic biases as evidence for ribosome remodeling.

中文翻译：

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分析健康和疾病中的核糖体重塑。

越来越多的证据表明核糖体积极调节蛋白质合成。然而，大部分证据都是间接的，这使得这一层基因调控在很大程度上未被探索，部分原因是方法学上的限制。事实上，审查证据表明常用的方法（例如转录组学）是不够的，因为编码核糖体蛋白（RP）的 mRNA 的变异性并不一定与 RP 变异性相对应。因此，应该通过允许直接定量 RP（最好是分离的核糖体）的方法来研究核糖体的蛋白质重塑。对此类方法进行了回顾，重点关注质谱分析并强调方法特定的偏差以及控制这些偏差的方法。有人认为，使用多种互补方法可以帮助减少将可重复的系统偏差解释为核糖体重塑证据的危险。