| Chapter title |
Secondary Metabolic Pathway-Targeted Metabolomics.
|
|---|---|
| Chapter number | 12 |
| Book title |
Nonribosomal Peptide and Polyketide Biosynthesis
|
| Published in |
Methods in molecular biology, January 2016
|
| DOI | 10.1007/978-1-4939-3375-4_12 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-3373-0, 978-1-4939-3375-4
|
| Authors |
Vizcaino, Maria I, Crawford, Jason M, Maria I. Vizcaino, Jason M. Crawford, Vizcaino, Maria I., Crawford, Jason M. |
| Abstract |
This chapter provides step-by-step methods for building secondary metabolic pathway-targeted molecular networks to assess microbial natural product biosynthesis at a systems level and to aid in downstream natural product discovery efforts. Methods described include high-resolution mass spectrometry (HRMS)-based comparative metabolomics, pathway-targeted tandem MS (MS/MS) molecular networking, and isotopic labeling for the elucidation of natural products encoded by orphan biosynthetic pathways. The metabolomics network workflow covers the following six points: (1) method development, (2) bacterial culture growth and organic extraction, (3) HRMS data acquisition and analysis, (4) pathway-targeted MS/MS data acquisition, (5) mass spectral network building, and (6) network enhancement. This chapter opens with a discussion on the practical considerations of natural product extraction, chromatographic processing, and enhanced detection of the analytes of interest within complex organic mixtures using liquid chromatography (LC)-HRMS. Next, we discuss the utilization of a chemometric platform, focusing on Agilent Mass Profiler Professional software, to run MS-based differential analysis between sample groups and controls to acquire a unique set of molecular features that are dependent on the presence of a secondary metabolic pathway. Using this unique list of molecular features, the chapter then details targeted MS/MS acquisition for subsequent pathway-dependent network clustering through the online Global Natural Products Social Molecular Networking (GnPS) platform. Genetic information, ionization intensities, isotopic labeling, and additional experimental data can be mapped onto the pathway-dependent network, facilitating systems biosynthesis analyses. The finished product will provide a working molecular network to assess experimental perturbations and guide novel natural product discoveries. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Australia | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Spain | 1 | 2% |
| Sweden | 1 | 2% |
| Germany | 1 | 2% |
| Brazil | 1 | 2% |
| Unknown | 38 | 90% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 7 | 17% |
| Student > Master | 5 | 12% |
| Researcher | 5 | 12% |
| Student > Bachelor | 4 | 10% |
| Student > Doctoral Student | 3 | 7% |
| Other | 7 | 17% |
| Unknown | 11 | 26% |
| Readers by discipline | Count | As % |
|---|---|---|
| Chemistry | 8 | 19% |
| Agricultural and Biological Sciences | 7 | 17% |
| Biochemistry, Genetics and Molecular Biology | 4 | 10% |
| Pharmacology, Toxicology and Pharmaceutical Science | 3 | 7% |
| Computer Science | 2 | 5% |
| Other | 6 | 14% |
| Unknown | 12 | 29% |