Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT.
Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT.
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在泥浆之前，使用蛋白酶剂通过蛋白质组均衡改善了低丰度蛋白的蛋白质组学指标。
DOI：
10.1021/pr200304u
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发表时间：
2011-08-05
影响因子：
4.4
通讯作者：
Yates, John R., III
中科院分区：
文献类型：
--
作者：
Fonslow, Bryan R.;Carvalho, Paulo C.;Academia, Katrina;Freeby, Steve;Xu, Tao;Nakorchevsky, Aleksey;Paulus, Aran;Yates, John R., III
理想情况下，鸟枪式蛋白质组学将有助于鉴定具有100%蛋白质序列覆盖率的整个蛋白质组。在现实中，细胞蛋白质组的大动态范围和复杂性导致对丰富蛋白质的过度采样，而来自低丰度蛋白质的多肽采样不足或仍未被检测到。我们测试了蛋白质组均衡技术ProteoMiner和多维蛋白质识别技术(MudPIT)，以确定蛋白质动态范围的均衡如何改进用于细胞蛋白质组分析的鸟枪式蛋白质组学方法。我们的结果表明，低丰度蛋白质的鉴定是通过两种机制改进的：(1)高丰度蛋白质的耗尽释放了通常由高丰度多肽占据的离子陷阱采样空间；(2)低丰度蛋白质的浓缩增加了对其相应的更丰富多肽的采样概率。由于来自低丰度蛋白质的多肽的前体强度增加，这两种机制也导致识别的多肽的数量和获得的MS/MS光谱的质量显著增加。从我们鉴定的蛋白质的大量数据集中，我们将促进蛋白质组均衡的主要物理化学因素归类为六肽库。这些结果表明，细胞蛋白质组动态范围的均衡化是一种很有前途的方法，可以在鸟枪式蛋白质组学实验中提高低丰度蛋白质鉴定的置信度、重复性和序列覆盖率，为提高蛋白质组覆盖率开辟了一条新的研究途径。
Ideally shotgun proteomics would facilitate the identification of an entire proteome with 100% protein sequence coverage. In reality, the large dynamic range and complexity of cellular proteomes results in oversampling of abundant proteins, while peptides from low abundance proteins are undersampled or remain undetected. We tested the proteome equalization technology, ProteoMiner, in conjunction with Multidimensional Protein Identification Technology (MudPIT) to determine how the equalization of protein dynamic range could improve shotgun proteomics methods for the analysis of cellular proteomes. Our results suggest low abundance protein identifications were improved by two mechanisms: (1) depletion of high abundance proteins freed ion trap sampling space usually occupied by high abundance peptides and (2) enrichment of low abundance proteins increased the probability of sampling their corresponding more abundant peptides. Both mechanisms also contributed to dramatic increases in the quantity of peptides identified and the quality of MS/MS spectra acquired due to increases in precursor intensity of peptides from low abundance proteins. From our large data set of identified proteins, we categorized the dominant physicochemical factors which facilitate proteome equalization with a hexapeptide library. These results illustrate that equalization of the dynamic range of the cellular proteome is a promising methodology to improve low abundance protein identification confidence, reproducibility, and sequence coverage in shotgun proteomics experiments, opening a new avenue of research for improving proteome coverage.
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算：一种用于提取和预处理光谱计数数据的计算工具，用于无标签的定量蛋白质组学分析。
影响因子：
3.4
作者：
Fermin, Damian;Basrur, Venkatesha;Yocum, Anastasia K.;Nesvizhskii, Alexey I.
通讯作者：
Nesvizhskii, Alexey I.
DOI：
10.1016/j.jchromb.2005.12.048
发表时间：
2006-03-20
影响因子：
3
作者：
Guerrier, L;Thulasiraman, V;Boschetti, E
通讯作者：
Boschetti, E
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
DOI：
10.1006/meth.1994.1029
发表时间：
1994-01-01
期刊：
Methods (Orlando)
影响因子：
--
作者：
McCormack, Ashley L.;Eng, Jimmy K.;Yates, John R., III
通讯作者：
Yates, John R., III
影响因子：
7.4
作者：
Liu, HB;Sadygov, RG;Yates, JR
通讯作者：
Yates, JR