Improved genome annotation through untargeted detection of pathway-specific metabolites.
Improved genome annotation through untargeted detection of pathway-specific metabolites.
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DOI：
10.1186/1471-2164-12-s1-s6
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发表时间：
2011-06-15
期刊：
影响因子：
4.4
通讯作者：
Northen T
中科院分区：
文献类型：
--
作者：
Bowen BP;Fischer CR;Baran R;Banfield JF;Northen T
基于质谱的代谢组学分析有可能补充基于序列的基因组注释方法，但前提是原始质谱数据可以与特定的代谢途径联系起来。在非靶向代谢组学中，检测到的化合物的测量质量用于定义化合物在化学空间中的位置，但质量测量的不确定性导致化学空间中的“简并性”，因为多个化学式对应于相同的测量质量。我们比较了两种方法来消除这些退化。一种方法依赖于天然同位素丰度，另一种方法依赖于使用稳定同位素标记（SIL）来直接确定C和N原子数。两者都依赖于对“化学空间”的组合探索，该空间由所有可能的化学式组成，化学式由生物学相关的化学元素组成。在MetaCyc数据库中管理的1532种代谢途径中，有412种含有具有该代谢途径特有的化学式的代谢物。因此，仅凭化学式就足以推断某些代谢途径的存在。从PubChem数据库中选择的248，928个独特的化学式中，超过95%至少有一个简并性，仅基于准确的质量信息。考虑天然同位素丰度的简并性降低到64%，但主要是分子量小于500 Da的公式，并且只有当相对同位素峰强度的误差小于10%时。通过SIL确定的精确C和N原子计数的知识能够降低简并性，允许确定55%的PubChem公式的独特化学式。为了便于将化学式分配给未知的质谱特征，可以对用氮（15N）或碳（13C）的稳定同位素均匀标记的培养物进行分析。这使得可以精确地计数每个分子中的碳和氮原子的数目，提供用于降低化学空间的简并性的稳健手段，并且因此获得在具有大于500 Da的质量的非靶向代谢组学中测量的特征的独特化学式，其中测量的同位素峰强度的相对误差大于10%，并且不使用依赖于启发式过滤的化学式生成器。这些化学式可以作为特定代谢途径存在的指标。
Mass spectrometry-based metabolomics analyses have the potential to complement sequence-based methods of genome annotation, but only if raw mass spectral data can be linked to specific metabolic pathways. In untargeted metabolomics, the measured mass of a detected compound is used to define the location of the compound in chemical space, but uncertainties in mass measurements lead to "degeneracies" in chemical space since multiple chemical formulae correspond to the same measured mass. We compare two methods to eliminate these degeneracies. One method relies on natural isotopic abundances, and the other relies on the use of stable-isotope labeling (SIL) to directly determine C and N atom counts. Both depend on combinatorial explorations of the "chemical space" comprised of all possible chemical formulae comprised of biologically relevant chemical elements. Of 1532 metabolic pathways curated in the MetaCyc database, 412 contain a metabolite having a chemical formula unique to that metabolic pathway. Thus, chemical formulae alone can suffice to infer the presence of some metabolic pathways. Of 248,928 unique chemical formulae selected from the PubChem database, more than 95% had at least one degeneracy on the basis of accurate mass information alone. Consideration of natural isotopic abundance reduced degeneracy to 64%, but mainly for formulae less than 500 Da in molecular weight, and only if the error in the relative isotopic peak intensity was less than 10%. Knowledge of exact C and N atom counts as determined by SIL enabled reduced degeneracy, allowing for determination of unique chemical formula for 55% of the PubChem formulae. To facilitate the assignment of chemical formulae to unknown mass-spectral features, profiling can be performed on cultures uniformly labeled with stable isotopes of nitrogen (15N) or carbon (13C). This makes it possible to accurately count the number of carbon and nitrogen atoms in each molecule, providing a robust means for reducing the degeneracy of chemical space and thus obtaining unique chemical formulae for features measured in untargeted metabolomics having a mass greater than 500 Da, with relative errors in measured isotopic peak intensity greater than 10%, and without the use of a chemical formula generator dependent on heuristic filtering. These chemical formulae can serve as indicators for the presence of particular metabolic pathways.