Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets.
Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets.
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DOI：
10.1021/acs.jproteome.2c00823
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发表时间：
2023-06-02
影响因子：
4.4
通讯作者：
Jones, Andrew R.
中科院分区：
文献类型：
--
作者：
Camacho, Oscar M.;Ramsbottom, Kerry A.;Collins, Andrew;Jones, Andrew R.
关键词：
磷酸化是一种翻译后修饰，由于其在许多生物过程中的相关性，引起了研究人员的极大兴趣。LC-MS/MS技术使高通量数据采集成为可能，研究声称识别和定位了数千个亚磷酸盐。亚磷酸盐的识别和定位来自不同的分析管道和评分算法，整个管道都嵌入了不确定性。对于许多流水线和算法，使用了任意阈值，但这些研究中实际的全局错误定位率知之甚少。最近，在已报道的肽谱匹配中，有人建议使用诱骗氨基酸来估计亚磷酸盐的全球错误定位率。在这里，我们描述了一个简单的管道，旨在通过客观地从肽谱匹配到肽样位点水平来最大化从这些研究中提取的信息，以及结合多项研究的结果，同时保持对错误定位率的跟踪。我们表明，该方法比目前使用更简单的机制来处理研究内和研究之间的亚磷酸盐识别冗余的过程更有效。在我们的案例研究中，使用了8个水稻磷酸蛋白质组数据集，使用我们的诱饵方法自信地识别了6368个独特的位置，而使用传统的阈值方法识别出了4687个错误定位率未知的位置。
Phosphorylation is a post-translational modification of great interest to researchers due to its relevance in many biological processes. LC-MS/MS techniques have enabled high-throughput data acquisition, with studies claiming identification and localization of thousands of phosphosites. The identification and localization of phosphosites emerge from different analytical pipelines and scoring algorithms, with uncertainty embedded throughout the pipeline. For many pipelines and algorithms, arbitrary thresholding is used, but little is known about the actual global false localization rate in these studies. Recently, it has been suggested to use decoy amino acids to estimate global false localization rates of phosphosites, among the peptide–spectrum matches reported. Here, we describe a simple pipeline aiming to maximize the information extracted from these studies by objectively collapsing from peptide–spectrum match to the peptidoform-site level, as well as combining findings from multiple studies while maintaining track of false localization rates. We show that the approach is more effective than current processes that use a simpler mechanism for handling phosphosite identification redundancy within and across studies. In our case study using eight rice phosphoproteomics data sets, 6368 unique sites were confidently identified using our decoy approach compared to 4687 using traditional thresholding in which false localization rates are unknown.
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影响因子：
3.4
作者：
Deutsch, Eric W.;Mendoza, Luis;Shteynberg, David;Farrah, Terry;Lam, Henry;Tasman, Natalie;Sun, Zhi;Nilsson, Erik;Pratt, Brian;Prazen, Bryan;Eng, Jimmy K.;Martin, Daniel B.;Nesvizhskii, Alexey I.;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
4.4
作者：
Hulstaert, Niels;Shofstahl, Jim;Perez-Riverol, Yasset
通讯作者：
Perez-Riverol, Yasset
水稻雌蕊磷酸化蛋白质组分析
影响因子：
3.4
作者：
Wang, Kun;Zhao, Yong;Yang, Pingfang
通讯作者：
Yang, Pingfang
影响因子：
3.4
作者：
Eng, Jimmy K.;Jahan, Tahmina A.;Hoopmann, Michael R.
通讯作者：
Hoopmann, Michael R.
影响因子：
7
作者：
Shteynberg, David;Deutsch, Eric W.;Nesvizhskii, Alexey I.
通讯作者：
Nesvizhskii, Alexey I.