How to use open-pFind in deep proteomics data analysis?- A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data.

生物物理学报:英文版 Pub Date : 2021-06-30 DOI:10.52601/bpr.2021.210004

Guangcan Shao, Yong Cao, Zhenlin Chen, Chao Liu, Shangtong Li, Hao Chi, Meng-Qiu Dong

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引用次数: 10

Abstract

High-throughput proteomics based on mass spectrometry (MS) analysis has permeated biomedical science and propelled numerous research projects. pFind 3 is a database search engine for high-speed and in-depth proteomics data analysis. pFind 3 features a swift open search workflow that is adept at uncovering less obvious information such as unexpected modifications or mutations that would have gone unnoticed using a conventional data analysis pipeline. In this protocol, we provide step-by-step instructions to help users mastering various types of data analysis using pFind 3 in conjunction with pParse for data pre-processing and if needed, pQuant for quantitation. This streamlined pParse-pFind-pQuant workflow offers exceptional sensitivity, precision, and speed. It can be easily implemented in any laboratory in need of identifying peptides, proteins, or post-translational modifications, or of quantitation based on ¹⁵N-labeling, SILAC-labeling, or TMT/iTRAQ labeling.

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如何在深度蛋白质组学数据分析中使用open-pFind ?-从质谱数据中严格鉴定和定量肽和蛋白质的协议。

基于质谱(MS)分析的高通量蛋白质组学已经渗透到生物医学科学中，并推动了许多研究项目。pFind 3是一个用于高速和深入蛋白质组学数据分析的数据库搜索引擎。pFind 3提供了一个快速开放的搜索工作流，它擅长发现不太明显的信息，比如使用传统的数据分析管道无法注意到的意外修改或突变。在本协议中，我们提供分步说明，帮助用户掌握各种类型的数据分析，使用pFind 3与pParse结合进行数据预处理，如果需要，使用pQuant进行定量。这种精简的pParse-pFind-pQuant工作流程提供了卓越的灵敏度，精度和速度。它可以在任何需要鉴定肽，蛋白质或翻译后修饰的实验室中轻松实现，或基于15n标记，silac标记或TMT/iTRAQ标记的定量。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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