metabolomics

Question 1

What is metabolomics?

Answer 1

study of concentrations of
every (or most) metabolites that can be measured in a particular cell)

Question 2

What can metabolomics be used to study

Answer 2

Carbohydrates, Amino acids, Lipids, Pollutants, Steroid hormones

Question 3

What is Discovery Metabolomics

Answer 3

Untargeted, examines tens of thousands of metabolites qualitatively to identify differences.

Question 4

What is Targeted Metabolomics

Answer 4

quantitatively analyzing a limited set of metabolites (tens or hundreds) with concentration standards, useful for precise concentration comparisons.

Question 5

What is Liquid Chromatography

Answer 5

Separates in a column for a chemical property,
* Detect and record an elution profile
* collect fractions if the goal is the purification of components

Question 6

The basic setup of LC

Answer 6

Solvents, Sample injections, column, detector to outflow

Question 7

HPLC?

Answer 7

uses sophisticated instruments operating at high pressures ex Reverse phase chromatography

Question 8

Mass Spectroscopy?

Answer 8

analyzes the eluted mixture, recording intensity for each m/z value. LC/MS is used for metabolomics to provide separation and mass-specific analysis.

Question 9

M/z Calculation for Ionized Molecule

Answer 9

The m/z value is calculated by dividing the ionized mass by the charge state

Question 10

Relationship between Mass Spectrum and Total Ion Chromatogram

Answer 10

The total ion chromatogram (TIC) shows the sum of intensities in the mass spectrum at each time point during liquid chromatography (LC). TIC has time on the x-axis and intensity on the y-axis, representing the overall amount of substances eluting at each moment.

Question 11

What heavy isotope is the greatest contributor to peaks with higher m/z values in the mass spectrum?

Answer 11

The peaks with higher m/z values are primarily influenced by the natural abundance of 13C, which constitutes approximately 1% of all carbon atoms. No other commonly found element in metabolites has a heavy isotope with such significant natural abundance.

Question 12

Ionization

Answer 12

charging a molecule
Deprotonation, Cationization, Protonation
Electron Capture
Electron ejection

Question 13

Time of Flight

Answer 13

Ions travel through field free region at a velocity
proportional to their m/z. Larger/Heavier = Longer time Smaller/Lighter = Shorter time
KE = ½ mv2

Question 14

Molecular Features- volume

Answer 14

the total area of all ions associated

Question 14

Principle Components Analysis
(PCA)

Answer 14

Quality Control, Visualization of Patterns. The closer samples are on the scatter plot,
the more similar they are

Question 15

PLS‐DA

Answer 15

statistical method, overfit data and grouping , more rigorous validation

Question 16

Hierarchical Clustering

Answer 16

visualize relationships, identify patterns

Question 17

Volcano plots

Answer 17

p-value vs Fold change, far from the center along the x-axis (high effect size) and high along the y-axis (high significance) are considered significantly changed.

Question 18

Correlation

Answer 18

Relationship between X and Y

Question 19

Regression

Answer 19

Predicts the value of a dependent variable based on the known value of the independent variable

Question 20

Random Forest:

Answer 20

a decision tree with the element of a
sampling technique in which we randomly
sample with replacement from the data
set.

Question 21

Machine Learning Tools: WGCNA
Weighted Gene Correlation Network
Analysis

Answer 21

identify groups of highly correlated compounds
that co-occur across your samples. Sorted into modules

Question 22

Arguably biggest issue in metabolomics

Answer 22

Compound identification

Question 23

limitations

Answer 23

Reproducibility
– Sample prep
– Quantitative platform (validation)
– QC and randomization
* False discovery rates
* Compound identification**
* Interpretation