评论“多阶段蛋白质组学搜索策略的无偏统计分析”。
Comment on "Unbiased statistical analysis for multi-stage proteomic search strategies".
机构信息
Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304, USA.
出版信息
J Proteome Res. 2011 Apr 1;10(4):2123-7. doi: 10.1021/pr101143m. Epub 2011 Feb 21.
Abstract
Everett et al. recently reported on a statistical bias that arises in the target-decoy approach to false discovery rate estimation in two-pass proteomics search strategies as exemplified by X!Tandem. This bias can cause serious underestimation of the false discovery rate. We argue here that the "unbiased" solution proposed by Everett et al., however, is also biased and under certain circumstances can also result in a serious underestimate of the FDR, especially at the protein level.
摘要
埃弗雷特等人最近报道了一种在双通蛋白质组学搜索策略（如 X!Tandem 中）的靶标-诱饵方法中出现的统计偏差，这种偏差会导致错误发现率的严重低估。我们在这里认为，埃弗雷特等人提出的“无偏”解决方案也是有偏差的，并且在某些情况下也会导致 FDR 的严重低估，尤其是在蛋白质水平上。
相似文献
1
Comment on "Unbiased statistical analysis for multi-stage proteomic search strategies".评论“多阶段蛋白质组学搜索策略的无偏统计分析”。
J Proteome Res. 2011 Apr 1;10(4):2123-7. doi: 10.1021/pr101143m. Epub 2011 Feb 21.
2
Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach.基于目标-诱饵法的鸟枪法蛋白质组学无偏错误发现率估计
J Proteome Res. 2017 Feb 3;16(2):393-397. doi: 10.1021/acs.jproteome.6b00144. Epub 2016 Dec 13.
3
False discovery rates in spectral identification.光谱识别中的假发现率。
BMC Bioinformatics. 2012;13 Suppl 16(Suppl 16):S2. doi: 10.1186/1471-2105-13-S16-S2. Epub 2012 Nov 5.
4
Decoy methods for assessing false positives and false discovery rates in shotgun proteomics.用于评估鸟枪法蛋白质组学中假阳性和错误发现率的诱饵方法。
Anal Chem. 2009 Jan 1;81(1):146-59. doi: 10.1021/ac801664q.
5
Calculation of False Discovery Rate for Peptide and Protein Identification.肽段和蛋白质鉴定的错误发现率计算
Methods Mol Biol. 2020;2051:145-159. doi: 10.1007/978-1-4939-9744-2_6.
6
Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.用于鸟枪法蛋白质组学的改进型错误发现率估计程序
J Proteome Res. 2015 Aug 7;14(8):3148-61. doi: 10.1021/acs.jproteome.5b00081. Epub 2015 Jul 27.
7
Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics.基于猪肉的食品清真蛋白质组学大规模串联质谱的比较数据库搜索引擎分析
J Proteomics. 2021 Jun 15;241:104240. doi: 10.1016/j.jprot.2021.104240. Epub 2021 Apr 21.
8
A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.一种用于大规模蛋白质组学数据集中蛋白质错误发现率估计的可扩展方法。
Mol Cell Proteomics. 2015 Sep;14(9):2394-404. doi: 10.1074/mcp.M114.046995. Epub 2015 May 17.
9
Challenging Targets or Describing Mismatches? A Comment on Common Decoy Distribution by Madej et al.有挑战性的目标还是描述不匹配？对 Madej 等人常见诱饵分布的评论
J Proteome Res. 2022 Dec 2;21(12):2840-2845. doi: 10.1021/acs.jproteome.2c00279. Epub 2022 Oct 28.
10
Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics.通用诱饵分布简化了鸟枪法蛋白质组学中的错误发现率估计
J Proteome Res. 2022 Feb 4;21(2):339-348. doi: 10.1021/acs.jproteome.1c00600. Epub 2022 Jan 6.
引用本文的文献
1
The Secret of Secrets: Carbonic Anhydrase Concentration in Lizards' Femoral Gland Secretions Is Tuned to Environmental Conditions.秘密中的秘密：蜥蜴股腺分泌物中的碳酸酐酶浓度与环境条件相适应。
Ecol Evol. 2025 Aug 21;15(8):e72023. doi: 10.1002/ece3.72023. eCollection 2025 Aug.
2
Harmful algal blooms are preceded by a predictable and quantifiable shift in the oceanic microbiome.有害藻华之前，海洋微生物群落会发生可预测和可量化的变化。
Nat Commun. 2025 Apr 29;16(1):3986. doi: 10.1038/s41467-025-59250-y.
3
Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.利用MS Annika 3.0进行全蛋白质组不可裂解交联鉴定揭示了秀丽隐杆线虫Box C/D复合物的结构。
Commun Chem. 2024 Dec 19;7(1):300. doi: 10.1038/s42004-024-01386-x.
4
Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach.通过 MiCId 增强工作流程鉴定抗生素耐药蛋白。一种基于质谱的蛋白质组学方法。
J Am Soc Mass Spectrom. 2022 Jun 1;33(6):917-931. doi: 10.1021/jasms.1c00347. Epub 2022 May 2.
5
Considerations for constructing a protein sequence database for metaproteomics.构建宏蛋白质组学蛋白质序列数据库的注意事项。
Comput Struct Biotechnol J. 2022 Jan 21;20:937-952. doi: 10.1016/j.csbj.2022.01.018. eCollection 2022.
6
Identification of MAMP-Responsive Plasma Membrane-Associated Proteins in Following Challenge with Different LPS Chemotypes from .在受到来自[具体来源]的不同脂多糖化学型刺激后，鉴定与MAMP反应相关的质膜相关蛋白。
Pathogens. 2020 Sep 25;9(10):787. doi: 10.3390/pathogens9100787.
7
Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry.通过串联质谱法对微生物进行稳健准确的鉴定和生物量估计。
J Am Soc Mass Spectrom. 2020 Jan 2;31(1):85-102. doi: 10.1021/jasms.9b00035. Epub 2019 Nov 20.
8
Morph-specific protein patterns in the femoral gland secretions of a colour polymorphic lizard.形态特异的蛋白模式在一种颜色多态蜥蜴的股腺分泌物中。
Sci Rep. 2019 Jun 10;9(1):8412. doi: 10.1038/s41598-019-44889-7.
9
Identification of Candidate Ergosterol-Responsive Proteins Associated with the Plasma Membrane of .鉴定与. 质膜相关的候选麦角固醇反应蛋白。
Int J Mol Sci. 2019 Mar 14;20(6):1302. doi: 10.3390/ijms20061302.
10
ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.ProteoStorm：一种超快的代谢组学数据库搜索框架。
Cell Syst. 2018 Oct 24;7(4):463-467.e6. doi: 10.1016/j.cels.2018.08.009. Epub 2018 Sep 26.
本文引用的文献
1
Unbiased statistical analysis for multi-stage proteomic search strategies.多阶段蛋白质组学搜索策略的无偏统计分析。
J Proteome Res. 2010 Feb 5;9(2):700-7. doi: 10.1021/pr900256v.
2
Reanalysis of Tyrannosaurus rex Mass Spectra.霸王龙质谱的重新分析。
J Proteome Res. 2009 Sep;8(9):4328-32. doi: 10.1021/pr900349r.
3
Improved ranking functions for protein and modification-site identifications.用于蛋白质和修饰位点鉴定的改进排序函数。
J Comput Biol. 2008 Sep;15(7):705-19. doi: 10.1089/cmb.2007.0119.
4
The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.Paragon算法是一种新一代搜索引擎，它使用序列温度值和特征概率从串联质谱中识别肽段。
Mol Cell Proteomics. 2007 Sep;6(9):1638-55. doi: 10.1074/mcp.T600050-MCP200. Epub 2007 May 27.
5
Validated MALDI-TOF/TOF mass spectra for protein standards.经验证的蛋白质标准品的基质辅助激光解吸电离飞行时间串联质谱（MALDI-TOF/TOF）质谱图
J Am Soc Mass Spectrom. 2007 May;18(5):850-5. doi: 10.1016/j.jasms.2007.01.010. Epub 2007 Feb 27.
6
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.用于提高质谱法大规模蛋白质鉴定可信度的靶标-诱饵搜索策略。
Nat Methods. 2007 Mar;4(3):207-14. doi: 10.1038/nmeth1019.
7
Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry.查找峰：一种用于串联质谱法蛋白质鉴定的从头测序与数据库搜索相结合的方法。
Anal Chem. 2007 Feb 15;79(4):1393-400. doi: 10.1021/ac0617013. Epub 2007 Jan 23.
8
Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides.鸟枪法蛋白质组学数据的动态谱质量评估与迭代计算分析：迈向更高效地鉴定翻译后修饰、序列多态性和新型肽段
Mol Cell Proteomics. 2006 Apr;5(4):652-70. doi: 10.1074/mcp.M500319-MCP200. Epub 2005 Dec 12.
9
A Heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results.一种用于根据Mascot数据库搜索结果为蛋白质鉴定分配错误发现率的启发式方法。
Mol Cell Proteomics. 2005 Jun;4(6):762-72. doi: 10.1074/mcp.M400215-MCP200. Epub 2005 Feb 9.
10
TANDEM: matching proteins with tandem mass spectra.串联：将蛋白质与串联质谱进行匹配。
Bioinformatics. 2004 Jun 12;20(9):1466-7. doi: 10.1093/bioinformatics/bth092. Epub 2004 Feb 19.
Zotero 插件