Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rua Professor Algacyr Munhoz Mader 3775, Cidade Industrial De Curitiba, Curitiba 81310-020, PR, Brazil.
Laboratory of Toxinology, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brazil 4036, Campus Maré, Rio de Janeiro 21040-361, RJ, Brazil.
Int J Mol Sci. 2024 Jan 18;25(2):1183. doi: 10.3390/ijms25021183.
SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database. We demonstrate the value of SpliceProt 2.0 to predict orthologous proteins between humans and murines based on transcript reconstruction, sequence annotation and detection at the transcriptome and proteome levels. In this release, the annotation data used in the reconstruction of transcripts based on the methodology of ternary matrices were acquired from new databases such as Ensembl, UniProt, and APPRIS. Another innovation implemented in the pipeline is the exclusion of transcripts predicted to be susceptible to degradation through the NMD pathway. Taken together, our repository and its applications represent a valuable resource for the proteogenomics community.
SpliceProt 2.0 是一个公共的蛋白质组学数据库，旨在列出人类、小鼠和大鼠蛋白质组中已知蛋白质和潜在新的蛋白质形式的序列。这个更新的存储库提供了更广泛的计算翻译蛋白质，并有助于例如，对参考 UniProtKB/SwissProt 数据库中不存在的剪接变体进行蛋白质组学验证。我们展示了 SpliceProt 2.0 的价值，基于转录重建、序列注释以及在转录组和蛋白质组水平上的检测，来预测人类和鼠类之间的同源蛋白质。在这个版本中，基于三元矩阵方法的转录本重建中使用的注释数据是从 Ensembl、UniProt 和 APPRIS 等新数据库中获取的。在管道中实施的另一个创新是排除了通过 NMD 途径预测易降解的转录本。总的来说，我们的存储库及其应用代表了蛋白质组学社区的一个有价值的资源。
