Examining Troughs in the Mass Distribution of All Theoretically Possible Tryptic Peptides

This work describes the mass distribution of all theoretically possibly tryptic peptides made of 20 amino acids, up to the mass of 3 kDa, with resolution of 0.001 Da. We characterize regions between the peaks of the distribution, including gaps (forbidden zones) and low-populated areas (quiet zones). We show how the gaps shrink over the mass range and when they completely disappear. We demonstrate that peptide compositions in quiet zones are less diverse than those in the peaks of the distribution and that by eliminating certain types of unrealistic compositions the gaps in the distribution may be increased. The mass distribution is generated using a parallel implementation of a recursive procedure that enumerates all amino acid compositions. It allows us to enumerate all compositions of tryptic peptides below 3 kDa in 48 min using a computer cluster with 12 Intel Xeon X5650 CPUs (72 cores). The results of this work can be used to facilitate protein identification and mass defect labeling in mass spectrometry-based proteomics experiments.

本研究阐述了由20种氨基酸构成的理论上可能的所有肽段的质量分布情况，涵盖质量上限至3 kDa，分辨率为0.001 Da。我们对分布曲线峰值之间的区域进行了特征化，包括间隙（禁止区域）和低密度区域（安静区域）。本研究揭示了随着质量范围的扩大，间隙如何逐渐缩小，以及它们何时完全消失。实验表明，安静区域中的肽段组成相较于分布曲线峰值区域的组成更为单一，通过消除某些不切实际的组成类型，分布曲线中的间隙可以得到扩大。该质量分布是通过并行实现的递归过程生成的，该过程枚举了所有氨基酸组成。利用配备12个Intel Xeon X5650 CPU（共72核心）的计算机集群，该过程可在48分钟内枚举出3 kDa以下的所有肽段组成。本研究的结果有助于促进基于质谱的蛋白质组学实验中的蛋白质鉴定和质量亏损标记。