A high confidence, manually validated human blood plasma protein reference set.
A high confidence, manually validated human blood plasma protein reference set.
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高信心，手动验证的人血浆蛋白参考集。
DOI：
10.1186/1755-8794-1-41
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发表时间：
2008-09-15
影响因子：
2.7
通讯作者：
Mann, Matthias
中科院分区：
文献类型：
--
作者：
Schenk, Susann;Schoenhals, Gary J.;de Souza, Gustavo;Mann, Matthias
人类血浆的巨大诊断潜力引起了人们对其内容编目的极大兴趣和努力，人类蛋白质组组织(HUPO)血浆蛋白质组计划(PPP)试点项目就是一个例子。由于在获得可靠的血浆蛋白质列表方面存在挑战，HuPo后来通过更严格的统计处理重新分析了他们自己的原始数据集，导致高置信度(至少95%)蛋白质列表与他们最初的发现相比大大减少。为了促进未来新的生物标志物的发现，充分发挥血浆的诊断潜力，我们认为仍然需要一个超高置信度(至少99%置信度)的血浆蛋白参考清单。为了解决血浆蛋白质组的复杂性和动态蛋白质浓度范围的问题，我们采用了线性离子陷阱-傅立叶变换(LTQ-FT)和线性离子陷阱-轨道捕捉(LTQ-Orbitrap)进行了质谱分析。这两种仪器都允许在低ppm范围内测量多肽质量。此外，我们使用了一个统计分数，允许使用串联质谱分析(MS3)的两个连续阶段的产品进行数据库肽鉴定搜索。MS3在亲本多肽中具有非常高的质量准确度，这使得多肽鉴定具有比通常实现的更高的置信度数量级。在这里，我们建立了一个由697个血浆蛋白组成的高置信度集合，并实现了每个蛋白质超过14个肽的高“平均序列覆盖率”，每个蛋白质的中位数为6个肽。所有被注释为属于免疫球蛋白家族的蛋白质以及其肽与免疫球蛋白序列完全匹配的所有假想蛋白质都被排除在该蛋白质列表之外。我们还比较了使用两种高端MS仪器以及使用不同的多肽和蛋白质分离方法的结果。此外，我们使用细胞定位信息对血浆蛋白质进行了表征，并将我们的蛋白质列表与其他来源的数据进行了比较，包括HuPo PPP数据集。一流的仪器与严格的验证标准相结合，产生了一套我们非常有信心的697种血浆蛋白，证明了极低的假肽识别率0.29%。
The immense diagnostic potential of human plasma has prompted great interest and effort in cataloging its contents, exemplified by the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) pilot project. Due to challenges in obtaining a reliable blood plasma protein list, HUPO later re-analysed their own original dataset with a more stringent statistical treatment that resulted in a much reduced list of high confidence (at least 95%) proteins compared with their original findings. In order to facilitate the discovery of novel biomarkers in the future and to realize the full diagnostic potential of blood plasma, we feel that there is still a need for an ultra-high confidence reference list (at least 99% confidence) of blood plasma proteins. To address the complexity and dynamic protein concentration range of the plasma proteome, we employed a linear ion-trap-Fourier transform (LTQ-FT) and a linear ion trap-Orbitrap (LTQ-Orbitrap) for mass spectrometry (MS) analysis. Both instruments allow the measurement of peptide masses in the low ppm range. Furthermore, we employed a statistical score that allows database peptide identification searching using the products of two consecutive stages of tandem mass spectrometry (MS3). The combination of MS3 with very high mass accuracy in the parent peptide allows peptide identification with orders of magnitude more confidence than that typically achieved. Herein we established a high confidence set of 697 blood plasma proteins and achieved a high 'average sequence coverage' of more than 14 peptides per protein and a median of 6 peptides per protein. All proteins annotated as belonging to the immunoglobulin family as well as all hypothetical proteins whose peptides completely matched immunoglobulin sequences were excluded from this protein list. We also compared the results of using two high-end MS instruments as well as the use of various peptide and protein separation approaches. Furthermore, we characterized the plasma proteins using cellular localization information, as well as comparing our list of proteins to data from other sources, including the HUPO PPP dataset. Superior instrumentation combined with rigorous validation criteria gave rise to a set of 697 plasma proteins in which we have very high confidence, demonstrated by an exceptionally low false peptide identification rate of 0.29%.
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影响因子：
12.3
作者：
Pilch B;Mann M
通讯作者：
Mann M
影响因子：
64.5
作者：
Foster, LJ;de Hoog, CL;Mann, M
通讯作者：
Mann, M
DOI：
10.1073/pnas.0405549101
发表时间：
2004-09-14
影响因子：
11.1
作者：
Olsen, JV;Mann, M
通讯作者：
Mann, M
影响因子：
4.4
作者：
Peng, JM;Elias, JE;Gygi, SP
通讯作者：
Gygi, SP
影响因子：
7
作者：
Olsen, JV;de Godoy, LMF;Mann, M
通讯作者：
Mann, M