胰蛋白酶与赖氨酸C端内切酶不同顺序酶切对蛋白质组样本制备的影响

Effects of Different Sequential Enzymatic Cleavage of Trypsin and LysC on Proteomic Sample Preparation

在基于质谱的蛋白质组学研究中,深度高效的蛋白质酶解是确保蛋白质被充分酶解,提升蛋白质鉴定深度(包括鉴定蛋白质数目以及蛋白质氨基酸序列覆盖率等)的关键。胰蛋白酶(trypsin)由于其能够特异性酶解精氨酸和赖氨酸羧基端,是基于质谱技术的蛋白质组学领域应用最为广泛的蛋白酶。然而,研究发现,胰蛋白酶对于赖氨酸残基的切割存在一定的遗漏酶切效率。因此,在实际蛋白质组学样本制备中,会采用胰蛋白酶和赖氨酸C端内切酶(LysC)联合使用的方式,确保赖氨酸残基的充分酶切。我们的研究发现,常用的LysC-Trypsin串联酶切的方式,会因首先加入的LysC对后续加入的胰蛋白酶进行切割,从而影响了胰蛋白酶对蛋白质样本的酶切效果。因此,本研究进行了LysC和胰蛋白酶串联酶切顺序的调整,即首先进行胰蛋白酶酶切,再加入LysC酶进行切割。本文全面比较了Trypsin-Trypsin(T-T)、LysC-Trypsin(L-T)和Trypsin-LysC(T-L)3种不同的顺序酶切方法对蛋白质样本制备质量的影响,结果表明,Trypsin-LysC顺序酶切方法在不增加实验成本的条件下,不仅获得最低的蛋白质赖氨酸/精氨酸遗漏酶切位点数目,而且酶解后得到的肽段氨基酸序列长度适中,使得Trypsin-LysC酶切后肽段样本更有利于反相色谱吸附和分离,以及串联质谱检测,从而最终显著提升样本中蛋白质的检测深度和蛋白质氨基酸序列覆盖率。本文工作为蛋白质样本的溶液内顺序酶切提供了新的技术方案和参考依据。

In mass spectrometry-based proteomics experiments,achieving high-throughput and efficient proteolytic digestion is crucial to ensure optimal protein cleavage and enhance the depth of protein identification(including the number of identified proteins and the coverage of protein amino acid sequences).Trypsin is the most widely used protease in mass spectrometry-based proteomics due to its ability to specifically cleave the carboxyl terminus of arginine and lysine.However,it was found that Trypsin has some missed enzymatic efficiency for the cleavage of lysine residues.Therefore,in actual proteomics sample preparation,a combination of Trypsin and LysC will be used to ensure adequate cleavage of lysine residues.Our study revealed that the commonly employed LysC-Trypsin tandem cleavage method exerts an impact on the enzymatic cleavage of protein samples by Trypsin due to the subsequent cleavage of Trypsin by initially added LysC.Consequently,we adjusted the order of LysC and Trypsin tandem digestion,with Trypsin cleavage being performed first followed by the addition of LysC to target any missed lysine residues.We comprehensively compared and analyzed three distinct sequential digestion methods,namely Trypsin-Trypsin(T-T),LysC-Trypsin(L-T),and Trypsin-LysC(T-L),in terms of their effects on protein sample preparation quality.The results demonstrated that the Trypsin-LysC sequential digestion approach not only minimizes missed protein lysine/arginine cleavage sites without increasing experimental costs,at the same time yielding peptides with a moderate amino acid sequence length.The use of Trypsin-LysC digestion enhances the adsorption and separation of peptide samples in RP-HPLC,as well as improves the depth of protein detection and amino acid sequence coverage during tandem mass spectrometry analysis.This research work offers a novel technical solution and serves as a valuable reference for proteome sample preparation.