Automated Data Extraction from In Situ Protein-Stable Isotope Probing Studies
Automated Data Extraction from In Situ Protein-Stable Isotope Probing Studies
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DOI：
10.1021/pr400633j
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发表时间：
2014-03-01
影响因子：
4.4
通讯作者：
Lipton, Mary S.
中科院分区：
文献类型：
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作者：
Slysz, Gordon W.;Steinke, Laurey;Lipton, Mary S.
蛋白质稳定同位素探测技术（protein-SIP）在揭示复杂微生物群落中的关键代谢类群方面具有很强的潜力。虽然迄今为止大多数蛋白质SIP工作都是在受控的实验室条件下进行的，以允许对靶生物进行广泛的同位素标记，但一个关键的应用将是在自然条件下短时间内对微生物群落进行原位研究，从而导致小程度的部分标记。限制大规模原位蛋白质-SIP研究的一个障碍是缺乏算法和软件来自动化处理来自此类研究的大量数据集。作为回应，我们开发了稳定同位素探测蛋白质提取资源软件（SIPPER），并将其应用于大规模提取和可视化的数据，从短期（3小时）蛋白质SIP实验进行原位光养细菌垫分离黄石国家公园。纳入软件的几个指标，使其能够支持详尽的分析复杂的复合同位素信封观察到的结果，少量的部分标签纳入。SIPPER还能够检测标记的分子种类，而无需任何预先鉴定。
Protein-stable isotope probing (protein-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. While most protein-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism(s), a key application will be in situ studies of microbial communities for short periods of time under natural conditions that result in small degrees of partial labeling. One hurdle restricting large-scale in situ protein-SIP studies is the lack of algorithms and software for automated data processing of the massive data sets resulting from such studies. In response, we developed Stable Isotope Probing Protein Extraction Resources software (SIPPER) and applied it for large-scale extraction and visualization of data from short-term (3 h) protein-SIP experiments performed in situ on phototrophic bacterial mats isolated from Yellowstone National Park. Several metrics incorporated into the software allow it to support exhaustive analysis of the complex composite isotopic envelope observed as a result of low amounts of partial label incorporation. SIPPER also enables the detection of labeled molecular species without the need for any prior identification.