摘要
基于串联质谱技术的蛋白质组学已经成为生命科学领域的重要工具,其中肽段的理论串联质谱图(通常也被称为二级谱图)预测问题在近年来广受关注.大量高质量质谱数据的积累和计算技术的发展为此问题的解决提供了有效途径.肽段的理论二级谱图预测的方法可以分为两大类,一类是基于物理模型的方法,即基于移动质子模型的方法,例如MassAnalyzer、MS-Simulator;另一类是基于机器学习的方法,包括集成学习相关算法和基于神经网络的方法,例如PeptideART、MS2PIP、MS2PBPI和p Deep等.本文对这两大类方法进行了整理和综述,并简要指出了目前理论谱图预测方法存在的一些不足,展望了未来的发展方向.
Tandem mass spectrometry(MS/MS)-based proteomics has become one of the most important tools in bioscience, and researchers now pay much attention to the prediction of MS/MS spectra for protein identification and quantification. With the accumulation of massive high-quality spectrum data and the development of computing technology, quite a few new methods were emerged to solve this problem. These methods can be divided into two catagories:mobile proton model-based methods, such as MassAnalyzer and MS-Simulator;and machine learning-based methods, including traditional machine learning and deep learning, such as PeptideART,MS2PIP, MS2PBPI and pDeep. In this paper, we investigated a wide variety of corresponding methods, and briefly pointed out the deficiencies of existing software tools, and suggested the future work.
作者
周撷璇
任睿
高婉铃
黄运有
曾文锋
孔德飞
郝天舒
张知非
詹剑锋
ZHOU Xie-Xuan;REN Rui;GAO Wan-Ling;HUANG Yun-You;ZENG Wen-Feng;KONG De-Fei;HAO Tian-Shu;ZHANG Zhi-Fei;ZHAN Jian-Feng(State Key Laboratory of Computer Architecture,Institute of Computing Technology(ICT),Chinese Academy of Sciences(CAS),Beijing 100190,China;Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences,Institute of Computing Techology(ICT),Chinese Academy of Sciences(CAS),Beijing 100190,China;University of Chinese Academy of Sciences,Beijing 100049,China;Department of Physiology and Pathophysiology,Capital Medical University,Beijing 100069,China)
出处
《生物化学与生物物理进展》
SCIE
CAS
CSCD
北大核心
2019年第2期169-180,共12页
Progress In Biochemistry and Biophysics
基金
国家重点研究发展计划(2016YFB1000605)资助项目~~
关键词
质谱
蛋白质组学
移动质子模型
机器学习
深度学习
mass spectrometry
proteomics
mobile proton model
machine learning
deep learning