一种使用PTMiner进行串联质谱开放或封闭搜索鉴定的蛋白质修饰的质量控制和定位的方案。

A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra.

作者信息

Cheng Zhiyuan, Song Ge, Fu Yan

机构信息

Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.

School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.

出版信息

Biophys Rep. 2022 Dec 31;8(5-6):269-281. doi: 10.52601/bpr.2022.220024.

DOI:10.52601/bpr.2022.220024

PMID:37287873

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10166509/

Abstract

In recent years, an open search of tandem mass spectra has greatly promoted the detection of post-translational modifications (PTMs) in shotgun proteomics. However, post-processing of the results from open searches remains an unsatisfactorily resolved problem, which hinders the open search mode from wide practical use. PTMiner is a software tool based on dedicated statistical algorithms for reliable filtering, localization and annotation of the modifications (mass shifts) detected by open search. Furthermore, PTMiner also supports quality control and re-localization of modifications identified by the traditional closed search. In this protocol, we describe how to use PTMiner for the two search modes. Currently, the search engines supported by PTMiner include pFind, MSFragger, MaxQuant, Comet, MS-GF + and SEQUEST.

摘要

近年来，串联质谱的开放搜索极大地促进了鸟枪法蛋白质组学中翻译后修饰（PTM）的检测。然而，开放搜索结果的后处理仍然是一个尚未得到令人满意解决的问题，这阻碍了开放搜索模式的广泛实际应用。PTMiner是一种基于专用统计算法的软件工具，用于对开放搜索检测到的修饰（质量位移）进行可靠的过滤、定位和注释。此外，PTMiner还支持对传统封闭搜索识别出的修饰进行质量控制和重新定位。在本方案中，我们描述了如何将PTMiner用于两种搜索模式。目前，PTMiner支持的搜索引擎包括pFind、MSFragger、MaxQuant、Comet、MS-GF+和SEQUEST。