Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement.

中文翻译：

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piNET：通用的Web平台，用于蛋白质组学数据的下游分析和可视化。

蛋白质组学的快速发展和蛋白质水平的生物系统的大规模概况分析，需要继续开发有效的计算工具来分析和解释蛋白质组学数据。在这里，我们介绍了piNET服务器，该服务器可促进定量蛋白质组学数据的集成注释，分析和可视化，重点是PTM网络以及与LINCS化学和遗传微扰签名库的集成，以提供进一步的机理和功能见解。服务器的主要输入由一组肽或蛋白质（可能具有PTM位点）及其相应的丰度值组成。几个相互关联的工作流程可用于生成：（i）交互式图形和表格，提供具有PTM位点的肽和蛋白质之间的全面注释和映射；（ii）高分辨率和交互式可视化的酶-底物网络，包括激酶及其磷酸肽靶标；（iii）映射和可视化LINCS签名连接性，以实现其目标PTM位点上游化学抑制剂或酶的基因敲低。piNET是使用模块化Spring-Boot JAVA平台构建的，它是一种快速，通用且易于使用的工具。Apache Lucene索引用于将肽快速映射到人，小鼠和其他常用的模型生物蛋白质组的UniProt条目中。以PTM为中心的网络分析结合了经过验证的酶与底物关系的PhosphoSitePlus，iPTMnet和SIGNOR数据库，通过DeepPhos预测和PhosphoSitePlus共有基序的基于序列的映射增强的激酶网络。使用iLINCS映射一致的LINCS签名。对于每个工作流程，可以使用RESTful API对应项以json格式以编程方式生成结果。该服务器可从http://pinet-server.org获得，它是免费的，并且对所有用户开放，而无需登录。