ESEI-Department of Computer Science, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas S/N 32004, Ourense, Spain.
CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain.
Nucleic Acids Res. 2017 Jul 3;45(W1):W265-W269. doi: 10.1093/nar/gkx389.
Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting software existed to facilitate such phylogeny inference. Hence, we developed the Peptidomes for Phylogenies (P4P) web tool, which enables the survey of similarities between microbial proteomes and simplifies the process of obtaining new biological insights into their phylogeny. P4P can be used to analyze different peptide datasets, i.e. bacteria, viruses, eukaryotic species or even metaproteomes. Also, it is able to work with whole proteome datasets and experimental mass-to-charge lists originated from mass spectrometers. The ultimate aim is to generate a valid and manageable list of peptides that have phylogenetic signal and are potentially sample-specific. Sample-to-sample comparison is based on a consensus peak set matrix, which can be further submitted to phylogenetic analysis. P4P holds great potential for improving phylogenetic analyses in challenging taxonomic groups, biomarker identification or epidemiologic studies. Notably, P4P can be of interest for applications handling large proteomic datasets, which it is able to reduce to small matrices while maintaining high phylogenetic resolution. The web server is available at http://sing-group.org/p4p.
肽组相似性分析使研究人员能够深入了解差异肽谱，提供了一种强大的工具来区分菌株特异性肽、真正的生物复制种内差异，甚至微生物表型变异。然而，目前还没有能够促进这种系统发育推断的计算肽指纹软件。因此，我们开发了用于系统发育的肽组（P4P）网络工具，它可以调查微生物蛋白质组之间的相似性，并简化获得有关其系统发育的新生物学见解的过程。P4P 可用于分析不同的肽数据集，例如细菌、病毒、真核生物甚至宏蛋白质组。它还能够处理来自质谱仪的整个蛋白质组数据集和实验质荷比列表。最终目标是生成具有系统发育信号且可能具有样本特异性的有效且可管理的肽列表。样本间比较基于共识峰集矩阵，该矩阵可以进一步提交给系统发育分析。P4P 在改进具有挑战性的分类群、生物标志物识别或流行病学研究中的系统发育分析方面具有巨大潜力。值得注意的是，对于处理大型蛋白质组数据集的应用，P4P 可能会感兴趣，因为它能够在保持高系统发育分辨率的同时将其减少到小矩阵。网络服务器可在 http://sing-group.org/p4p 上获得。
