Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. In this study, we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. These NCPs showed distinct characteristics compared with conventional peptides and were derived from introns, 3′ UTRs, 5′ UTRs, junctions, and intergenic regions. Furthermore, our results showed that translation events in unannotated transcripts occur more broadly than previously thought. In addition, we found that dozens of maize NCPs are enriched within regions associated with phenotypic variations and domestication selection, indicating that they potentially are involved in genetic regulation of complex traits and domestication in maize. Taken together, our study developed an integrated peptidogenomic pipeline for large-scale identification of NCPs in plants, which would facilitate global characterization of NCPs from other plants. The identification of large-scale NCPs in both monocot (maize) and dicot (Arabidopsis) plants indicates that a large portion of plant genome can be translated into biologically functional molecules, which has important implications for functional genomic studies.

非常规肽（NCP）包括小的开放阅读框编码的肽，在基本生物学过程中起关键作用。在这项研究中，我们使用高通量质谱技术开发了一条整合的肽基因组学流水线，以探查定制的六帧翻译数据库，并将其应用于植物中NCP的大规模鉴定。在玉米中共明确鉴定出1993和1860个NCP。和拟南芥， 分别。与常规肽相比，这些NCP表现出独特的特征，并衍生自内含子，3'UTR，5'UTR，连接点和基因间区域。此外，我们的结果表明，未注释的成绩单中的翻译事件发生的范围比以前认为的要广泛。此外，我们发现在表型变异和驯化选择相关的区域内，数十个玉米NCP富集，表明它们潜在地参与了玉米复杂性状的遗传调控和驯化。综上所述，我们的研究开发了一种整合的肽基因组学流水线，用于大规模鉴定植物中的NCP，这将有助于全球表征其他植物中的NCP。单子叶植物（玉米）和双子叶植物中大型NCP的鉴定（拟南芥植物表明植物基因组的大部分可以被翻译成具有生物学功能的分子，这对功能基因组研究具有重要意义。