Expanding the Use of Spectral Libraries in Proteomics.
Expanding the Use of Spectral Libraries in Proteomics.
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DOI：
10.1021/acs.jproteome.8b00485
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发表时间：
2018-12-07
影响因子：
4.4
通讯作者：
Röst H
中科院分区：
文献类型：
--
作者：
Deutsch EW;Perez-Riverol Y;Chalkley RJ;Wilhelm M;Tate S;Sachsenberg T;Walzer M;Käll L;Delanghe B;Böcker S;Schymanski EL;Wilmes P;Dorfer V;Kuster B;Volders PJ;Jehmlich N;Vissers JPC;Wolan DW;Wang AY;Mendoza L;Shofstahl J;Dowsey AW;Griss J;Salek RM;Neumann S;Binz PA;Lam H;Vizcaíno JA;Bandeira N;Röst H
2017年Dagstuhl计算蛋白质组学研讨会为广泛讨论肽串联质谱谱库的生成和使用的现状和未来方向提供了机会。它们在蛋白质组学中的应用正在缓慢增长，但该领域存在着多种挑战，必须解决这些挑战，以进一步增加光谱库和相关技术的采用。主要瓶颈是缺乏高质量和全面的库，以及将光谱库搜索纳入现有工作流程的普遍困难。有几种现有的光谱库格式，但没有一个捕获令人满意的元数据水平;因此，合乎逻辑的下一个改进是设计一个更先进的，蛋白质组学标准计划批准的光谱库格式，可以编码所有所需的元数据。该小组讨论了一系列元数据需求，这些元数据需求被组织成三种完整性或质量的名称，暂时称为青铜、银和黄金。元数据可以在四个不同的粒度级别上进行组织：在集合（库）级别上，在单个条目（肽离子）级别上，在峰（碎片离子）级别上，以及在峰注释级别上。讨论了以一致的方式编码质量修饰的策略以及编码高质量和常见但尚未鉴定的光谱的要求。该小组还讨论了相关主题，包括比较两个光谱的策略，为库生成代表性光谱的技术，为目标工作流程选择最佳特征离子的方法，以及将两个或多个库合并为一个库的问题。我们在这里提出了一个审查这一领域和社区必须解决的挑战，以加快通过光谱库在蛋白质组学数据集的常规分析。
The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none capture a satisfactory level of metadata; therefore a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly-seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
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影响因子：
3.7
作者：
Handy K;Rosen J;Gillan A;Smith R
通讯作者：
Smith R
影响因子：
3
作者：
Jeong K;Kim S;Bandeira N
通讯作者：
Bandeira N
影响因子：
5.8
作者：
Degroeve, Sven;Martens, Lennart
通讯作者：
Martens, Lennart
影响因子：
7
作者：
Bouyssie, David;Dubois, Marc;Monsarrat, Bernard
通讯作者：
Monsarrat, Bernard
影响因子：
4.4
作者：
Craig, R;Cortens, JP;Beavis, RC
通讯作者：
Beavis, RC