A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.
A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.
复制标题
小蛋白质的发现和表征的实用指南使用质谱。
DOI：
10.1128/jb.00353-21
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发表时间：
2022-01-18
影响因子：
3.2
通讯作者：
Langer JD
中科院分区：
文献类型：
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作者：
Ahrens CH;Wade JT;Champion MM;Langer JD
最多 ∼50 个氨基酸的小蛋白质是生命各个领域中丰富的一类生物分子。然而，由于其大小固有的挑战，它们经常在基因组注释中被遗漏，并且很难使用标准实验方法来识别和表征。因此，即使在经过充分研究的原核模型生物体中，我们仍然了解很少的小蛋白质。质谱 (MS) 在小蛋白质的发现、验证和功能表征方面具有巨大潜力。然而，由于典型蛋白质组学工作流程每个步骤（即样品制备、蛋白酶消化、液相色谱、MS 数据采集和数据分析）的局限性，标准 MS 方法不太适合识别已知和新型小蛋白质。在这里，我们概述了用于小蛋白质发现和验证的主要基于 MS 的工作流程和生物信息学管道。特别强调提高小蛋白质检测和数据质量所需的调整。我们讨论了小蛋白质的公正检测和感兴趣的小蛋白质的靶向分析。最后，我们提供了优先考虑新型小蛋白质的指南，并对具有进一步改善小蛋白质的全面发现和表征的特殊潜力的方法进行了展望。
Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
影响因子：
4.4
作者：
Payne SH;Huang ST;Pieper R
通讯作者：
Pieper R
PGP：用于MPI簇，高灌注批次群集和多层工作站的平行原核蛋白质组学管道。
DOI：
10.1093/bioinformatics/btu051
发表时间：
2014-05-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Tovchigrechko A;Venepally P;Payne SH
通讯作者：
Payne SH