ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.
ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites.
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Promex：用于蛋白质和蛋白质磷酸化位点的质谱参考数据库。
DOI：
10.1186/1471-2105-8-216
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发表时间：
2007-06-23
影响因子：
3
通讯作者：
Weckwerth, Wolfram
中科院分区：
文献类型：
--
作者：
Hummel, Jan;Niemann, Michaela;Wienkoop, Stefanie;Schulze, Waltraud;Steinhauser, Dirk;Selbig, Joachim;Walther, Dirk;Weckwerth, Wolfram
在过去的十年中，建立了对蛋白质、RNA和代谢物进行大规模全基因组分析的技术，并开发了数据库解决方案来管理生成的数据集。戈尔姆代谢物数据数据库(GMD)代表了这样一种努力，即使这些数据广泛可用，并将生物系统的不同分子水平相互连接起来。随着根据现有数据进行数据解释变得越来越重要，这些举措是当前和未来系统生物学的重要组成部分。基于LC-IT-MS(LC-IT-MS)建立了一个由实验衍生的胰酶多肽产物离子谱组成的质谱库。对来自拟南芥、莱茵衣藻、紫花苜蓿和紫花苜蓿的蛋白质样品进行了分析。该数据库目前有4,557个人工验证的光谱，与来自1,367个蛋白质的4,226个独特多肽相关联，作为一个不断增长的参考数据集，可用于对未表征的生物样品中的蛋白质进行鉴定和定量。对于多肽鉴定，基于最近发表的多肽质量指纹图谱研究，实施了几种算法，并测试了假阳性和阴性比率。一种考虑匹配相关性分数的强度分布的算法被发现产生了最好的结果。为了验证概念，将胰酶叶蛋白消化的LC-IT-MS分析转换为mzData格式，并在质谱库中进行搜索。还测试了质谱库在鉴定磷酸化胰蛋白酶多肽方面的应用。我们纳入了拟南芥蛋白质的体内磷酸化位点，发现与基于基因组的搜索算法相比，识别性能有所提高。ProMEX的蛋白质鉴定与其他水平的生物组织，如代谢物、途径和转录本数据有关。该数据库还通过BioMoby与注释和分类服务相连接。ProMEX蛋白质/多肽数据库代表了一个质谱库，具有匹配未知样品以进行蛋白质鉴定的能力。该数据库允许基于元数据进行文本搜索，例如样品的实验信息、质谱仪参数或唯一的蛋白质识别符，如AGI代码。ProMEX将蛋白质组学数据与包括代谢物、途径和转录信息在内的其他水平的分子组织相结合，因此可能成为植物系统生物学研究的有用资源。ProMEX质谱库位于。
In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadly available and to interconnect the different molecular levels of a biological system. As data interpretation in the light of already existing data becomes increasingly important, these initiatives are an essential part of current and future systems biology. A mass spectral library consisting of experimentally derived tryptic peptide product ion spectra was generated based on liquid chromatography coupled to ion trap mass spectrometry (LC-IT-MS). Protein samples derived from Arabidopsis thaliana, Chlamydomonas reinhardii, Medicago truncatula, and Sinorhizobium meliloti were analysed. With currently 4,557 manually validated spectra associated with 4,226 unique peptides from 1,367 proteins, the database serves as a continuously growing reference data set and can be used for protein identification and quantification in uncharacterized biological samples. For peptide identification, several algorithms were implemented based on a recently published study for peptide mass fingerprinting and tested for false positive and negative rates. An algorithm which considers intensity distribution for match correlation scores was found to yield best results. For proof of concept, an LC-IT-MS analysis of a tryptic leaf protein digest was converted to mzData format and searched against the mass spectral library. The utility of the mass spectral library was also tested for the identification of phosphorylated tryptic peptides. We included in vivo phosphorylation sites of Arabidopsis thaliana proteins and the identification performance was found to be improved compared to genome-based search algorithms. Protein identification by ProMEX is linked to other levels of biological organization such as metabolite, pathway, and transcript data. The database is further connected to annotation and classification services via BioMoby. The ProMEX protein/peptide database represents a mass spectral reference library with the capability of matching unknown samples for protein identification. The database allows text searches based on metadata such as experimental information of the samples, mass spectrometric instrument parameters or unique protein identifier like AGI codes. ProMEX integrates proteomics data with other levels of molecular organization including metabolite, pathway, and transcript information and may thus become a useful resource for plant systems biology studies. The ProMEX mass spectral library is available at .
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影响因子：
46.9
作者：
Washburn, MP;Wolters, D;Yates, JR
通讯作者：
Yates, JR
影响因子：
3.6
作者：
Morgenthal, Katja;Wienkoop, Stefanie;Weckwerth, Wolfram
通讯作者：
Weckwerth, Wolfram
DOI：
10.1016/1044-0305(94)87009-8
发表时间：
1994-09-01
影响因子：
3.2
作者：
STEIN, SE;SCOTT, DR
通讯作者：
SCOTT, DR
影响因子：
5.8
作者：
Steinhauser, D;Usadel, B;Kopka, J
通讯作者：
Kopka, J
影响因子：
7.4
作者：
Liu, HB;Sadygov, RG;Yates, JR
通讯作者：
Yates, JR