sean Flashcards
(59 cards)
- What is the primary reason for using GC/LC-MS in metabolomics?
A) It provides real-time visualization of metabolic pathways
B) It enables selective qualitative and quantitative analysis of metabolites
C) It eliminates the need for data preprocessing
D) It is the only technique available for metabolomics
B) It enables selective qualitative and quantitative analysis of metabolites
- What key challenge does metabolomics data preprocessing address?
A) Removing biologically significant signals
B) Correcting for peak drift and noise reduction
C) Increasing data redundancy for better visualization
D) Eliminating the need for machine learning models
B) Correcting for peak drift and noise reduction
- What is the main purpose of using retention time correction in metabolomics data preprocessing?
A) To detect all metabolites present in the sample
B) To compare retention times with internal standards and correct for peak drift
C) To eliminate irrelevant metabolite peaks
D) To perform spectral deconvolution
B) To compare retention times with internal standards and correct for peak drift
- Which of the following is NOT a limitation of GC/LC-MS in metabolomics?
A) High cost of analysis materials
B) Limited ability to identify novel metabolites
C) Requires long sample preparation times (several weeks)
D) Potential for instrumental bias
C) Requires long sample preparation times (several weeks)
- Which software is commonly used for metabolomics data preprocessing?
A) MZmine3, MAVEN, and XCMS
B) Excel and SPSS
C) GeneMapper and Galaxy
D) BLAST and FASTQC
A) MZmine3, MAVEN, and XCMS
- Which approach is used in targeted metabolomics for metabolite identification?
A) Comparing spectra against public online databases only
B) Using internal authentic standards for direct comparison
C) Manual peak detection using retention times
D) Excluding metabolites that do not match existing pathways
B) Using internal authentic standards for direct comparison
- Why is quality control (QC) essential in metabolomics data processing?
A) To determine variance and remove low-quality data
B) To visualize metabolic pathways directly
C) To generate synthetic metabolite datasets
D) To replace the need for retention time correction
A) To determine variance and remove low-quality data
- What is the primary goal of data normalization in metabolomics?
A) To introduce systematic bias for data clustering
B) To eliminate the need for mass spectrometry calibration
C) To reduce systematic bias and technical variation
D) To generate new metabolites computationally
C) To reduce systematic bias and technical variation
- What statistical method is used in metabolomics to control for false positives in multiple testing?
A) Bonferroni correction
B) Simple p-value thresholding
C) Regression analysis
D) Euclidean distance clustering
A) Bonferroni correction
- Why is a volcano plot used in metabolomics analysis?
A) To replace PCA in statistical modeling
B) To identify significant metabolite changes while accounting for fold change and p-values
C) To measure retention times across multiple samples
D) To compare metabolic pathways directly
B) To identify significant metabolite changes while accounting for fold change and p-values
- What is the main purpose of Principal Component Analysis (PCA) in metabolomics?
A) To identify individual metabolites in complex samples
B) To visualize overall patterns and clustering in metabolic data
C) To predict unknown metabolite functions
D) To separate targeted and untargeted metabolomics data
B) To visualize overall patterns and clustering in metabolic data
- What do the axes represent in a PCA plot?
A) Sample ID on the X-axis and metabolite intensity on the Y-axis
B) Two or more principal components that explain the variance in the dataset
C) Retention time on the X-axis and peak intensity on the Y-axis
D) Fold change on the X-axis and p-value on the Y-axis
B) Two or more principal components that explain the variance in the dataset
- In a PCA plot, what does it mean if two sample clusters are far apart?
A) They share identical metabolic profiles
B) They exhibit significant metabolic differences
C) They have undergone the same preprocessing corrections
D) They were analyzed using the same mass spectrometer
B) They exhibit significant metabolic differences
- In a PCA plot, what would tightly clustered QC samples indicate?
A) The assay has poor reproducibility
B) The experimental design is flawed
C) The quality of data is high
D) The samples have been incorrectly labeled
C) The quality of data is high
- What statistical approach does Partial Least Squares Discriminant Analysis (PLS-DA) use that differs from PCA?
A) PLS-DA focuses on maximizing group separation, whereas PCA focuses on variance explanation
B) PCA is used for classification, whereas PLS-DA is only for visualization
C) PLS-DA eliminates batch effects, whereas PCA does not
D) PCA removes outliers, while PLS-DA does no
Answer: A) PLS-DA focuses on maximizing group separation, whereas PCA focuses on variance explanation
- Below is a PCA plot with three clusters (A, B, C). Which of the following conclusions is most accurate?
(Graph not provided, but assume three well-separated clusters in PCA space)
A) Groups A and B are highly similar, while Group C is metabolically distinct
B) All three groups have identical metabolic profiles
C) PCA does not provide information about metabolic differences
D) Group C represents technical error rather than biological variation
A) Groups A and B are highly similar, while Group C is metabolically distinct
- What key challenge exists in metabolomics data integration with other omics datasets?
A) The inability to generate metabolic pathways
B) Unclear or inconsistent annotation in public databases
C) The lack of high-throughput technologies
D) The absence of statistical methods for validation
Answer: B) Unclear or inconsistent annotation in public databases
- What is a major future challenge in metabolomics data visualization?
A) The lack of free bioinformatics tools
B) The difficulty of integrating multi-omics data into a single clear visualization
C) The inability to perform statistical corrections
D) The excessive number of data points in mass spectrometry
B) The difficulty of integrating multi-omics data into a single clear visualization
- Which of the following is a major challenge in metabolomics studies?
A) Cells are always in the same metabolic state
B) Metabolomics experiments are free from variability
C) Cellular processes occur at different time points, making data interpretation difficult
D) Omics studies do not require experimental controls
C) Cellular processes occur at different time points, making data interpretation difficult
- What is the primary function of metabolomics in cancer research?
A) To analyze cell morphology changes
B) To identify key metabolites and interrogate pathways activated in cancer samples
C) To sequence the entire genome of tumor cells
D) To measure gene expression profiles only
Answer: B) To identify key metabolites and interrogate pathways activated in cancer samples
- Which two technologies are most frequently used for metabolomics data acquisition?
A) MALDI-TOF and Western Blot
B) NMR and RNA-seq
C) LC-MS and GC-MS
D) qPCR and Microarrays
Answer: C) LC-MS and GC-MS
- What is the role of ionization in mass spectrometry?
A) To fragment molecules into neutral atoms
B) To convert neutral molecules into charged ions for detection
C) To separate metabolites based on their size
D) To enhance the volatility of metabolites
Answer: B) To convert neutral molecules into charged ions for detection
- What advantage does Raman spectroscopy provide in metabolomics?
A) It requires large sample sizes
B) It detects non-polar metabolites more effectively
C) It does not require sample preparation
D) It can analyze metabolic changes in live cells
Answer: D) It can analyze metabolic changes in live cells
