Applied Biosciences, Macquarie University, Sydney, NSW, Australia.
Curr Protoc. 2022 Jul;2(7):e506. doi: 10.1002/cpz1.506.
With evidence emerging that the microbiome has a role in the onset of many human diseases, including cancer, analyzing these microbial communities and their proteins (i.e., the metaproteome) has become a powerful research tool. The Trans-Proteomic Pipeline (TPP) is a free, comprehensive software suite that facilitates the analysis of mass spectrometry (MS) data. By utilizing available microbial proteomes, TPP can identify microbial proteins and species, with an acceptable peptide false-discovery rate (FDR). An application to a publicly available oral cancer dataset is presented as an example to identify the viral metaproteome on the oral cancer invasive tumor front. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Collection of data and resources Basic Protocol 2: Analysis of MS data using TPP Basic Protocol 3: Analysis of TPP output using R in RStudio.
随着越来越多的证据表明微生物组在许多人类疾病（包括癌症）的发病中起作用，分析这些微生物群落及其蛋白质（即宏蛋白质组）已成为一种强大的研究工具。跨蛋白质组分析管道（Trans-Proteomic Pipeline，TPP）是一个免费的、全面的软件套件，可促进质谱（MS）数据的分析。通过利用可用的微生物蛋白质组，TPP 可以鉴定微生物蛋白和物种，肽假阳性率（FDR）可接受。本文以一个公开的口腔癌数据集为例，介绍了如何在口腔癌侵袭性肿瘤前缘识别病毒宏蛋白质组。© 2022 作者。 Wiley Periodicals LLC 出版的《当代协议》。 基本方案 1：数据和资源的收集 基本方案 2：使用 TPP 分析 MS 数据 基本方案 3：在 RStudio 中使用 R 分析 TPP 输出。
