Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
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DOI：
10.1021/acs.jproteome.9b00542
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发表时间：
2019-12-01
影响因子：
4.4
通讯作者：
Omenn, Gilbert S.
中科院分区：
文献类型：
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作者：
Deutsch, Eric W.;Lane, Lydie;Omenn, Gilbert S.
人类蛋白质组组织（HUPO）的人类蛋白质组计划（HPP）制定了自2016年以来一直适用的质谱（MS）数据解释指南。这些指导方针有助于确保新出现的完整人类蛋白质组草案高度准确，并且具有低数量的假阳性蛋白质鉴定。在这里，我们根据过去一年与更广泛的HPP社区的讨论，对这些指南进行了更新。修订后的准则3.0解决了几个主要和次要的已确定差距。对主要核对清单的标题和分项目进行了重新编排，并对相关准则进行了分组。我们已经为新兴的数据独立采集（DIA）MS工作流程和使用由HUPO蛋白质组学标准倡议（PSI）开发的新的通用谱标识符（USI）系统添加了指南。此外，我们讨论了标准HPP管道的更新，用于收集HPP中所有蛋白质的MS证据，包括对最小证据的改进。我们提出了一个新的计划，将MassIVE-KB纳入下一个（HPP 2020）周期的HPP管道，以便更全面地覆盖公共MS数据集。主要核对表按标题和分项重新编排，相关准则也进行了分组。总而言之，HPP MS数据解释指南的2.1版已经很好地发挥了作用，并且这个及时更新的3.0版将有助于HPP接近其收集和管理所有预测的类似于由人类基因组编码的20，000种人类蛋白质的翻译和表达的MS证据的目标。
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on discussions with the wider HPP community over the past year. The revised Guidelines 3.0 address several major and minor identified gaps. The main checklist has been reorganized under headings and subitems and related guidelines have been grouped. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well and this timely update version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted similar to 20,000 human proteins encoded by the human genome.