Proteomics, metabolomics and functionomics applications MCQs With Answer

Introduction: Proteomics, metabolomics and functionomics applications MCQs With Answer is designed for M.Pharm students seeking a focused, application-oriented review of modern omics techniques in pharmacology. This quiz collection emphasizes real-world applications: drug target discovery, biomarker identification, ADME/Tox profiling, pathway analysis, and systems-level functional interpretation. Questions span analytical platforms (LC-MS/MS, NMR, GC-MS), quantitative strategies (label-free, SILAC, iTRAQ, MRM), data processing (DIA vs DDA, FDR, normalization), and integrative approaches (fluxomics, pharmacometabolomics, interactomics). Each MCQ reinforces conceptual understanding and practical decision-making needed for experimental design and interpretation in research and regulatory contexts.

Q1. Which mass spectrometry acquisition strategy allows reproducible, comprehensive quantitation by fragmenting all precursor ions within predefined m/z windows, making it useful for large-scale proteomics?

• Data-dependent acquisition (DDA)
• Data-independent acquisition (DIA)
• Selected reaction monitoring (SRM)
• Top-down MS

Correct Answer: Data-independent acquisition (DIA)

Q2. In a SILAC experiment for quantitative proteomics, what is the primary mechanism that enables relative quantification between experimental conditions?

• Chemical labeling of peptides after digestion
• Metabolic incorporation of heavy isotopic amino acids into proteins
• Label-free spectral counting
• Post-translational modification enrichment

Correct Answer: Metabolic incorporation of heavy isotopic amino acids into proteins

Q3. Which technique is most appropriate for high-sensitivity, targeted quantitation of a defined set of drug metabolites in plasma during ADME studies?

• Untargeted LC-MS metabolomics
• GC-MS with electron ionization for volatile profiling
• Triple quadrupole LC-MS using MRM/SRM transitions
• NMR spectroscopy for structural elucidation

Correct Answer: Triple quadrupole LC-MS using MRM/SRM transitions

Q4. In metabolomics, what is the key advantage of NMR over mass spectrometry for certain applications?

• Higher sensitivity for low-abundance metabolites
• Absolute quantitation without extensive calibration standards
• Better separation of isomeric compounds without derivatization
• Higher throughput for thousands of metabolites

Correct Answer: Absolute quantitation without extensive calibration standards

Q5. Which bioinformatic approach is commonly used to reduce false positives when identifying peptides from MS/MS spectra?

• Principal component analysis (PCA)
• Target-decoy database search to estimate FDR
• Hierarchical clustering of spectral counts
• Metabolite set enrichment analysis (MSEA)

Correct Answer: Target-decoy database search to estimate FDR

Q6. Which sample preparation strategy improves detection of membrane proteins and hydrophobic drug targets for proteomic analysis?

• Soluble fraction enrichment by mild buffer wash
• Use of strong ionic detergents with subsequent cleanup (e.g., SDS removal or SP3)
• Direct trypsin digestion of intact cells without lysis
• Size-exclusion chromatography only

Correct Answer: Use of strong ionic detergents with subsequent cleanup (e.g., SDS removal or SP3)

Q7. Pharmacometabolomics aims to predict drug response by analyzing baseline metabolic profiles. Which statistical method is most appropriate to reduce dimensionality and visualize group separation before modeling?

• Multiple t-tests without correction
• Principal component analysis (PCA)
• Kaplan–Meier survival analysis
• BLAST sequence alignment

Correct Answer: Principal component analysis (PCA)

Q8. Which label-based quantitative proteomics method allows multiplexing of several samples in one LC-MS run by tagging peptides with isobaric labels?

• SILAC
• iTRAQ/TMT
• Label-free spectral counting
• MALDI imaging

Correct Answer: iTRAQ/TMT

Q9. In metabolomics data quality control, which practice helps monitor instrument performance and correct batch effects?

• Using different extraction solvents for each batch
• Including pooled QC samples and analyzing them periodically
• Only analyzing case samples and ignoring controls
• Randomly shuffling sample identities post-analysis

Correct Answer: Including pooled QC samples and analyzing them periodically

Q10. Functionomics often integrates omics data to infer biological function. Which network analysis metric helps identify highly connected hub proteins that may represent potential drug targets?

• Retention time index
• Degree centrality
• Mass-to-charge ratio
• Signal-to-noise ratio

Correct Answer: Degree centrality

Q11. Which metabolite identification approach provides structural information through fragmentation patterns and is essential when authentic standards are unavailable?

• Retention time matching only
• MS/MS spectral interpretation and library matching
• UV absorbance profiling
• Protein sequence alignment

Correct Answer: MS/MS spectral interpretation and library matching

Q12. For phosphoproteomics aimed at studying drug effects on signaling, which enrichment method is commonly used to isolate phosphorylated peptides prior to LC-MS?

• Hydrophobic interaction chromatography
• Immobilized metal affinity chromatography (IMAC) or TiO2 enrichment
• Size-exclusion purification
• Dialysis against PBS

Correct Answer: Immobilized metal affinity chromatography (IMAC) or TiO2 enrichment

Q13. In fluxomics, which experimental approach traces metabolic pathway activity by following incorporation of labeled isotopes (e.g., 13C) into metabolites?

• Untargeted metabolite fingerprinting
• Stable isotope-resolved metabolomics (SIRM) or isotope tracing
• Northern blot analysis
• Western blot quantification of enzymes

Correct Answer: Stable isotope-resolved metabolomics (SIRM) or isotope tracing

Q14. Which public database is especially useful for linking metabolites and metabolic pathways relevant to drug metabolism and toxicity studies?

• Protein Data Bank (PDB)
• Human Metabolome Database (HMDB) and KEGG pathway resources
• GenBank nucleotide archive
• UniProt protein annotation only

Correct Answer: Human Metabolome Database (HMDB) and KEGG pathway resources

Q15. Data-independent acquisition coupled with spectral libraries enables peptide-centric quantitation. What is a major limitation if spectral libraries are incomplete for a given organism or condition?

• Improved discovery of novel proteoforms
• Reduced ability to identify and quantify peptides not represented in the library
• Elimination of the need for chromatographic separation
• Automatic correction of post-translational modifications

Correct Answer: Reduced ability to identify and quantify peptides not represented in the library

Q16. In untargeted metabolomics, which normalization approach helps account for differences in sample concentration and analytical variation when comparing plasma samples?

• Normalization to total ion current (TIC) or probabilistic quotient normalization
• Normalization by random noise addition
• Using unnormalized raw intensities only
• Normalization by DNA content

Correct Answer: Normalization to total ion current (TIC) or probabilistic quotient normalization

Q17. Which proteomic strategy is best suited to directly identify intact proteoforms including combinations of PTMs and sequence variants?

• Bottom-up proteomics with tryptic peptides
• Top-down proteomics analyzing intact proteins by high-resolution MS
• Shotgun metabolomics
• Single-cell RNA sequencing

Correct Answer: Top-down proteomics analyzing intact proteins by high-resolution MS

Q18. When integrating proteomics and metabolomics for mechanism-of-action studies, what is a key analytical step to link molecular changes to perturbed pathways?

• Only report lists of altered molecules without context
• Pathway enrichment analysis and mapping changes onto metabolic and signaling networks
• Rely solely on fold-change thresholds without statistical testing
• Exclude post-translational modifications from consideration

Correct Answer: Pathway enrichment analysis and mapping changes onto metabolic and signaling networks

Q19. Which technique enables spatially resolved proteomics or metabolomics in tissue sections to study drug distribution and local biochemical effects?

• Shotgun LC-MS of whole tissue homogenates exclusively
• MALDI imaging mass spectrometry or LC-MS imaging approaches
• Sanger sequencing of tissue RNA
• Flow cytometry of dissociated cells only

Correct Answer: MALDI imaging mass spectrometry or LC-MS imaging approaches

Q20. In designing an omics experiment to discover predictive biomarkers for adverse drug reactions, which experimental principle is most critical to ensure valid downstream inference?

• Small sample size with no replication is acceptable
• Careful cohort selection, adequate sample size, randomization, and independent validation
• Omit quality control and batch randomization to save costs
• Only analyze cases and ignore confounding clinical variables

Correct Answer: Careful cohort selection, adequate sample size, randomization, and independent validation

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