Proteomics MCQs — Part 1 (Q1–Q25)

Q1. Proteomics primarily studies:

A. DNA sequence variations
B. RNA expression profiles
C. The entire set of proteins and their dynamics in a system ✅
D. Metabolic pathways only

A: DNA = genomics.
B: RNA = transcriptomics.
C: Proteomics focuses on identity, abundance, PTMs, interactions, and localization of proteins.
D: Metabolomics covers metabolites, not proteins.

Q2. The classic workflow of bottom-up proteomics begins with:

A. Direct MS of intact proteins
B. Protease digestion of proteins into peptides ✅
C. Edman degradation of peptides
D. Crosslinking proteins in vivo

A: That’s top-down.
B: Proteins are enzymatically digested (often with trypsin) → peptides analyzed by LC-MS/MS.
C: Edman is sequencing, not the MS workflow.
D: Crosslinking is for interaction mapping.

Q3. Trypsin cleaves peptide bonds:

A. After Asp/Glu
B. After Lys or Arg (except when followed by Pro) ✅
C. After aromatic residues
D. Before Lys/Arg

A: Asp/Glu are acidic; not trypsin’s specificity.
B: Trypsin is the standard protease due to predictable cleavage and MS-friendly peptides.
C/D: Incorrect specificity.

Q4. In 2D-PAGE, proteins are separated based on:

A. Isoelectric point then molecular weight ✅
B. Charge only
C. Hydrophobicity only
D. Molecular weight then isoelectric point

A: First dimension IEF (pI), second dimension SDS-PAGE (MW).
B/C/D: Do not describe 2D-PAGE correctly.

Q5. The soft ionization method well-suited for large biomolecules mixed with matrix crystals is:

A. Electron ionization
B. MALDI (Matrix-Assisted Laser Desorption/Ionization) ✅
C. Chemical ionization
D. FAB

A/C: Harsh, mostly small molecules.
B: MALDI gently ionizes peptides/proteins; often coupled to TOF analyzers.
D: Older method; less common now.

Q6. Which ionization method produces multiply charged ions ideal for LC-MS of peptides?

A. APCI
B. ESI (Electrospray Ionization) ✅
C. MALDI
D. EI

A: APCI suits small/medium nonpolar molecules.
B: ESI generates multiple charges, placing peptides/proteins in MS m/z range.
C: MALDI usually singly charged.
D: EI is too harsh.

Q7. In tandem MS (MS/MS), the fragmentation step typically occurs in:

A. Source
B. Collision cell (CID/HCD) producing b/y ions ✅
C. Detector
D. Vacuum pump

A: Source creates precursor ions.
B: Collisions fragment selected precursors; fragments reveal sequence.
C/D: Not where fragmentation is induced.

Q8. Label-free quantification commonly relies on:

A. Radioactive labeling
B. Peak area/intensity or spectral counting ✅
C. iTRAQ isobaric tags
D. SILAC isotopes in culture

A: Rare in modern proteomics.
B: LFQ compares signal intensity or PSM counts across runs.
C/D: Those are labeling strategies.

Q9. SILAC stands for:

A. Stable Ion Labeling of Amino Chains
B. Stable Isotope Labeling by/with Amino acids in Cell culture ✅
C. Simple Isotope Labeling of All Cells
D. Stable Ionization Labeling for Accurate Counting

A/C/D: Not the correct expansion.
B: Cells incorporate heavy amino acids (e.g., ^13C6-Lys/Arg) for in vivo labeling.

Q10. iTRAQ/TMT reagents enable:

A. Enrichment of phosphopeptides only
B. Multiplexed, isobaric tagging for relative quantification ✅
C. Absolute quantification only
D. Top-down sequencing

A: Phospho-enrichment uses TiO₂/IMAC.
B: Isobaric tags label peptides; reporter ions in MS/MS yield relative abundances across samples.
C: Absolute needs internal standards.
D: Not a top-down method.

Q11. A major challenge in proteomics compared to genomics is:

A. Lack of bioinformatics tools
B. Wide dynamic range and PTM diversity ✅
C. Proteins do not ionize
D. Proteins are fewer than genes

A: Tools exist but complexity is high.
B: Protein abundances span >6–10 orders; PTMs create many proteoforms.
C: Many do ionize with ESI/MALDI.
D: Proteoforms outnumber genes.

Q12. Shotgun proteomics refers to:

A. Top-down MS of intact proteins
B. Affinity purification only
C. Global bottom-up LC-MS/MS of complex digests ✅
D. Western blot screening

A: Opposite approach.
C: Digest mixture → LC-MS/MS → database search to identify proteins.

Q13. False Discovery Rate (FDR) control in peptide identification is often achieved using:

A. Only manual validation
B. Target–decoy database strategy ✅
C. Higher spray voltage
D. Increasing collision energy

A: Not scalable.
B: Searching against decoy sequences estimates false positives to set FDR (e.g., 1%).
C/D: Instrument settings, not statistics.

Q14. A proteotypic peptide is:

A. Any peptide that fragments well
B. Peptide uniquely mapping to a single protein ✅
C. Peptide with missed cleavages
D. Peptide only seen in MALDI

A: Desirable but not defining.
B: Used for confident protein ID/quantification because it’s unique.
C/D: Irrelevant.

Q15. In phosphoproteomics, a common enrichment strategy is:

A. C18 desalting only
B. IMAC or TiO₂ affinity for phosphopeptides ✅
C. Size exclusion chromatography
D. Cation exchange exclusively

A: Not selective for phospho.
B: Immobilized metal affinity (Fe³⁺/Ga³⁺) or TiO₂ captures phosphorylated peptides.
C/D: Not standard for specific enrichment.

Q16. Top-down proteomics provides:

A. Analysis of intact proteoforms including PTM combinations ✅
B. Only peptide-level info
C. No mass accuracy advantage
D. Faster than bottom-up in all cases

A: Intact MS preserves full PTM patterns and sequence variants.
B: That’s bottom-up.
C: High-res MS gives excellent accuracy.
D: Often more demanding.

Q17. A volcano plot in quantitative proteomics typically displays:

A. Mass vs charge
B. Fold-change vs statistical significance (–log10 p-value) ✅
C. Retention time vs intensity
D. pI vs MW

A/C/D: Other plots.
B: Highlights significantly up/down-regulated proteins.

Q18. To minimize missed cleavages during digestion, you should:

A. Lower pH to 1
B. Use chymotrypsin
C. Optimize trypsin ratio, time, and buffer (pH ~8) with denaturants ✅
D. Add strong oxidants

A: Denatures trypsin.
B: Different specificity.
C: Proper denaturation (urea), reduction/alkylation, and conditions improve completeness.
D: Damages peptides.

Q19. DIA/SWATH MS acquisition differs from DDA because it:

A. Ignores fragment ions
B. Fragments all ions within wide m/z windows for comprehensive sampling ✅
C. Requires isotope labels
D. Cannot quantify proteins

A: Uses fragments extensively.
B: DIA is unbiased; later deconvolution with spectral libraries.
C: Works label-free or labeled.
D: DIA is highly quantitative.

Q20. For absolute quantification of a protein by LC-MS, a standard approach is:

A. Spectral counting only
B. Stable-isotope labeled internal standard peptides (AQUA/SIS) ✅
C. Coomassie staining calibration
D. Western blot densitometry

A: Semi-quantitative.
B: Known amounts of heavy peptides enable absolute copy number estimation.
C/D: Not MS-based absolute methods.

Q21. Post-translational modifications (PTMs) include all EXCEPT:

A. Phosphorylation
B. Ubiquitination
C. Glycosylation
D. Transcription ✅

A–C: Classic PTMs.
D: Transcription makes RNA, not a protein modification.

Q22. Protein–protein interactions can be mapped by:

A. qPCR
B. Yeast two-hybrid, co-IP/MS, crosslinking MS ✅
C. Southern blot
D. HPLC UV only

A/C/D: Not PPI methods.
B: Standard techniques for interaction discovery and validation.

Q23. A common database search engine for peptide identification is:

A. Bowtie
B. Mascot/Sequest/Andromeda ✅
C. BLASTn
D. STAR

A/D: Read aligners for genomics.
B: These score peptide-spectrum matches (PSMs) against protein databases.
C: Nucleotide similarity tool.

Q24. Dynamic range in proteomics refers to:

A. The range of m/z the instrument can scan
B. Span of protein/peptide abundances measurable in a sample ✅
C. Difference between b and y ions
D. Number of gradient steps in LC

A: Instrumental scan range, not the biological range.
B: Biological samples can span 10⁶–10¹⁰ in abundance, challenging detection.
C/D: Not definitions of dynamic range.

Q25. SPR (Surface Plasmon Resonance) is used to measure:

A. Protein secondary structure
B. Label-free binding kinetics (k_on, k_off, K_D) ✅
C. Peptide mass only
D. Protein phosphorylation sites

A: CD/FTIR assess secondary structure.
B: SPR quantifies real-time molecular interactions and affinities.
C/D: MS/phospho-MS do those tasks.

Proteomics MCQs — Part 2 (Q26–Q50)

Q26. The term interactome refers to:

A. All metabolic pathways in a cell
B. All genes in an organism
C. The complete set of protein–protein interactions ✅
D. All small molecules

A: That’s the metabolome.
B: That’s the genome.
C: Interactome = full network of protein interactions.
D: Metabolome covers metabolites.

Q27. Which separation method is typically used before LC-MS to reduce sample complexity?

A. Capillary electrophoresis
B. High-performance liquid chromatography (HPLC) ✅
C. Western blotting
D. Immunohistochemistry

A: CE is used but less common in proteomics.
B: HPLC fractionates peptides before MS for higher sensitivity.
C/D: Detection methods, not preparative separations.

Q28. Spectral counting in proteomics is a method for:

A. PTM mapping
B. Protein folding studies
C. Relative quantification of protein abundance ✅
D. Protein purification

A: Requires site-specific analysis.
B: Folding studied by CD/NMR.
C: More spectra = higher abundance estimate.
D: Not quantification.

Q29. Protein microarrays are mainly used for:

A. RNA sequencing
B. High-throughput detection of protein interactions or antibodies ✅
C. DNA hybridization
D. Peptide sequencing

A/C/D: Related to genomics, not proteomics.
B: Arrays test many proteins/antibodies in parallel.

Q30. Which is an affinity-based proteomics technique?

A. SDS-PAGE
B. Co-immunoprecipitation (Co-IP) ✅
C. MALDI-TOF
D. Size exclusion chromatography

A/D: Size-based separations.
B: Antibody captures protein with its binding partners → identify by MS.
C: MS, not affinity-based.

Q31. The term secretome refers to:

A. The entire genome
B. All proteins secreted by a cell or tissue ✅
C. All cytoplasmic proteins
D. The nuclear proteome

A: DNA, not proteins.
B: Secretome = extracellular proteins, important in signaling.
C/D: Sub-proteomes, but not secretome.

Q32. Which analytical technique is most suitable for protein secondary structure determination?

A. MALDI-TOF
B. Circular dichroism (CD) spectroscopy ✅
C. LC-MS/MS
D. SDS-PAGE

A/C/D: Not structural tools.
B: CD spectroscopy detects α-helices, β-sheets, random coils.

Q33. Post-translational modifications (PTMs) such as phosphorylation are often enriched using:

A. Western blotting
B. Immobilized Metal Affinity Chromatography (IMAC) ✅
C. ELISA
D. Gel electrophoresis

A/C/D: Detection methods.
B: IMAC (Fe³⁺, Ga³⁺) selectively enriches phosphopeptides for MS.

Q34. Which bioinformatics resource is widely used for protein sequence analysis?

A. GenBank
B. UniProt ✅
C. PDB
D. KEGG

A: DNA sequences.
B: UniProt is the largest curated protein sequence database.
C: Protein structures.
D: Pathways.

Q35. The sub-proteome localized to mitochondria is called:

A. Cytoplasmic proteome
B. Nuclear proteome
C. Mitochondrial proteome ✅
D. Secretome

A/B/D: Other sub-proteomes.
C: Mitochondrial proteome = all proteins functioning in mitochondria.

Q36. Western blotting detects proteins based on:

A. DNA hybridization
B. RNA probe binding
C. Antibody–antigen recognition ✅
D. Mass-to-charge ratios

A/B: DNA/RNA detection.
C: Protein separated by SDS-PAGE, detected by specific antibodies.
D: MS detection, not Western.

Q37. Which isotope labeling method is commonly used in quantitative proteomics?

A. RFLP
B. SILAC (Stable Isotope Labeling by Amino acids in Cell culture) ✅
C. AFLP
D. qPCR

A/C/D: DNA-based methods.
B: SILAC incorporates heavy amino acids into proteins for quantitative MS.

Q38. MALDI-TOF measures:

A. Protein folding kinetics
B. Antigen–antibody binding
C. Mass-to-charge ratios of peptides/proteins ✅
D. DNA replication

A/B/D: Not what MALDI-TOF does.
C: MALDI-TOF = soft ionization + TOF analyzer → m/z detection.

Q39. Proteogenomics integrates:

A. Genomics with metabolomics
B. Proteomics data with genome annotation ✅
C. Transcriptomics with proteomics only
D. Clinical trials with genomics

A: Wrong combination.
B: Proteogenomics improves gene models using proteomics evidence.
C: Too narrow.
D: Not definition.

Q40. Which proteomic technique is often used to study cell signaling pathways?

A. qPCR
B. Phosphoproteomics ✅
C. Southern blot
D. FISH

A/C/D: DNA/RNA-focused.
B: Phosphorylation events regulate signaling, studied via phosphoproteomics.

Q41. Which database contains 3D structures of proteins?

A. GenBank
B. PDB (Protein Data Bank) ✅
C. UniProt
D. Pfam

A: DNA.
B: PDB stores protein/nucleic acid 3D structures.
C: Sequences.
D: Protein domains.

Q42. Label-free quantification relies on:

A. Isotope incorporation
B. Radioactive tags
C. Peptide ion intensities or spectral counts ✅
D. DNA probes

A/B/D: Label-based or non-protein tools.
C: LFQ compares MS signal intensities across samples.

Q43. Top-down proteomics analyzes:

A. Only RNA transcripts
B. Intact proteins directly by MS ✅
C. Peptides after digestion
D. Only secondary structures

A/D: Not proteomics.
B: Top-down = intact proteins → preserve PTM patterns.
C: Bottom-up approach.

Q44. The peptidome is defined as:

A. All genomic sequences
B. All lipids
C. All peptides present in a biological sample ✅
D. All carbohydrate chains

A: Genome.
B: Lipidome.
C: Peptidome = natural peptides (digestion products, signaling peptides).
D: Glycome.

Q45. The dynamic range of proteins in plasma spans:

A. 10²
B. 10³
C. 10¹⁰ or more ✅
D. 10⁵

A/B/D: Underestimate.
C: Plasma protein abundances span 10 orders of magnitude, challenging detection.

Q46. Affinity tags like His-tag or FLAG-tag are used for:

A. DNA sequencing
B. Protein purification and detection ✅
C. RNA hybridization
D. Protein degradation

A/C/D: Not tags’ purpose.
B: Tags facilitate affinity chromatography or immunodetection.

Q47. Which proteomics method uses antibody-coated chips?

A. MALDI-TOF
B. Protein microarray ✅
C. qPCR
D. SDS-PAGE

A/C/D: Not antibody chip-based.
B: Protein microarrays detect interactions/abundance using immobilized antibodies.

Q48. Which proteomics strategy is best to detect low-abundance transcription factors?

A. Coomassie-stained 1D gel
B. Enrichment followed by LC-MS/MS ✅
C. Agarose gel electrophoresis
D. UV spectroscopy

A/C/D: Insufficient sensitivity.
B: Enrichment with antibodies/chromatography + LC-MS/MS increases sensitivity.

Q49. A volcano plot in proteomics shows:

A. Protein charge vs size
B. Protein mass vs abundance
C. Fold-change vs statistical significance ✅
D. pH vs retention time

A/B/D: Not correct.
C: Volcano plots highlight significantly regulated proteins.

Q50. Which proteomics workflow analyzes all proteins in a tissue without bias?

A. Western blotting
B. ELISA
C. Discovery (shotgun) proteomics ✅
D. Targeted proteomics

A/B: Target specific proteins.
C: Discovery/shotgun = unbiased global analysis.
D: Quantifies selected proteins only.

Proteomics MCQs — Part 3 (Q51–Q75)

Q51. Which technique measures real-time protein–protein binding kinetics?

A. ELISA
B. Surface Plasmon Resonance (SPR) ✅
C. SDS-PAGE
D. Northern blot

A: ELISA detects proteins but not real-time binding.
B: SPR quantifies on-rate (k_on), off-rate (k_off), and affinity (K_D).
C/D: Separation/detection methods, not kinetics.

Q52. The proteoform concept describes:

A. Genes with multiple exons
B. Different molecular forms of a protein from one gene (splicing, PTMs, variants) ✅
C. Protein isoforms only from gene duplication
D. Only phosphorylated proteins

A: Splicing explains part of it.
B: Proteoform = all variants of a protein (splicing, SNPs, PTMs).
C/D: Too narrow.

Q53. Which proteomics approach is used for targeted quantification?

A. Shotgun discovery proteomics
B. Selected Reaction Monitoring (SRM/MRM) ✅
C. Western blotting
D. 2D-PAGE

A: Global analysis, not targeted.
B: SRM/MRM tracks selected peptides with high reproducibility.
C/D: Less precise, not MS-based quantification.

Q54. Which proteomics technique involves labeling proteins with fluorescent dyes before 2D gel separation?

A. Western blot
B. Difference Gel Electrophoresis (DIGE) ✅
C. Blue-native PAGE
D. ELISA

A/D: Immunoassays.
B: DIGE compares multiple protein samples labeled with different dyes on the same 2D gel.
C: Different separation purpose.

Q55. A heat map in proteomics usually represents:

A. Molecular weight distribution
B. DNA sequences
C. Relative abundance of proteins across samples ✅
D. Protein secondary structure

A/D: Not abundance.
C: Heat maps visualize abundance differences (color-coded).
B: For nucleotides, not proteomics.

Q56. Which database is specialized for protein–protein interactions?

A. PDB
B. STRING ✅
C. UniProt
D. KEGG

A: Protein structures.
B: STRING compiles predicted and known protein interactions.
C: Protein sequences.
D: Pathways.

Q57. Glycoproteomics focuses on:

A. Proteins bound to DNA
B. Protein glycosylation patterns and structures ✅
C. Lipid modifications of proteins
D. Phosphorylation events

A/D: Not glycosylation.
B: Glycoproteomics studies N-/O-linked glycans and functions.
C: Lipidation is separate.

Q58. Which technique measures protein 3D structure at atomic resolution?

A. SDS-PAGE
B. X-ray crystallography ✅
C. LC-MS/MS
D. ELISA

A/C/D: Detection/analysis, not atomic resolution.
B: X-ray crystallography provides detailed 3D protein structures.

Q59. Which high-resolution technique is increasingly used for large protein complexes?

A. Southern blot
B. Cryo-electron microscopy (Cryo-EM) ✅
C. PCR
D. qRT-PCR

A/C/D: DNA/RNA methods.
B: Cryo-EM reveals structures of huge complexes (e.g., ribosomes).

Q60. Interactomics is most closely related to:

A. Genomics
B. Proteomics of protein–protein interaction networks ✅
C. Transcriptomics
D. Epigenomics

A/C/D: Other omics.
B: Interactomics = mapping and studying protein interaction networks.

Q61. Which proteomics technique separates proteins in their native state?

A. Blue Native PAGE (BN-PAGE) ✅
B. SDS-PAGE
C. 2D-DIGE
D. Western blot

A: Correct → separates intact protein complexes.
B: Denaturing detergent used.
C: Denaturing gel.
D: Immunodetection after denaturation.

Q62. Which ion types are most commonly observed in peptide fragmentation (CID)?

A. a and c ions
B. b and y ions ✅
C. x and z ions
D. Neutral losses only

A/C: Produced in ETD/ECD methods.
B: CID/HCD yields b (N-terminal) and y (C-terminal) ions.
D: Neutral loss is secondary.

Q63. Dynamic proteomics studies:

A. Protein folding
B. Temporal changes in protein expression/localization ✅
C. Genomic sequences
D. RNA transcription

A/C/D: Not dynamic proteomics.
B: Dynamic proteomics tracks changes over time (e.g., cell cycle).

Q64. Which MS technique is best for high-mass accuracy and resolution?

A. Quadrupole
B. TOF
C. Orbitrap ✅
D. Ion trap

A/B/D: Used widely but moderate resolution.
C: Orbitrap achieves ultra-high resolution and ppm-level accuracy.

Q65. Label-free proteomics is advantageous because:

A. Proteins always ionize equally
B. No isotopic labeling required, cheaper and simpler ✅
C. It requires less bioinformatics
D. It avoids peptide digestion

A/D: Not true.
B: LFQ is cost-effective but needs careful normalization.
C: Actually needs complex analysis.

Q66. SWATH-MS is a data acquisition method that:

A. Measures DNA copy number
B. Requires radioactive labels
C. Collects fragment data for all peptides across wide m/z windows ✅
D. Detects only the most abundant peptides

A/B/D: Not correct.
C: SWATH-MS (DIA) captures all fragment data comprehensively.

Q67. A post-translational modification (PTM) that regulates protein degradation is:

A. Phosphorylation
B. Ubiquitination ✅
C. Glycosylation
D. Hydroxylation

A: Regulates activity.
B: Ubiquitin marks proteins for proteasome degradation.
C/D: Different regulatory roles.

Q68. The Human Proteome Project (HPP) aims to:

A. Map all RNAs
B. Sequence entire genomes
C. Identify and characterize all human proteins ✅
D. Build phylogenetic trees

A/B/D: Different projects.
C: HPP = global effort to characterize the full human proteome.

Q69. Phosphoproteomics provides insights into:

A. DNA repair
B. Cell signaling pathways regulated by phosphorylation ✅
C. Protein folding chaperones
D. Carbohydrate metabolism only

A/D: Indirect.
C: Folding is separate.
B: Phosphorylation controls kinases, signaling, cascades.

Q70. Which type of chromatography separates proteins based on net surface charge?

A. Size exclusion
B. Ion exchange chromatography ✅
C. Affinity chromatography
D. Hydrophobic interaction

A: Size only.
B: Ion exchange separates cations/anions based on charge differences.
C/D: Different mechanisms.

Q71. Which of the following enriches glycoproteins for analysis?

A. IMAC
B. Lectin affinity chromatography ✅
C. SDS-PAGE
D. HPLC

A: Phosphopeptides.
B: Lectins bind glycan structures, enriching glycoproteins.
C/D: Not selective for glycans.

Q72. A major limitation of 2D gel electrophoresis is:

A. It cannot separate proteins
B. Poor representation of very hydrophobic or very large/small proteins ✅
C. It requires mass spectrometry
D. It does not resolve by charge

A: False.
B: Membrane proteins and extremes in size/pI are underrepresented.
C: Can be used standalone.
D: Charge separation is part of 2D gels.

Q73. Cross-linking mass spectrometry (XL-MS) helps to:

A. Quantify absolute protein amounts
B. Determine spatial proximity of protein residues and interactions ✅
C. Identify only RNA-binding proteins
D. Map DNA sequences

A/C/D: Incorrect.
B: XL-MS identifies interaction sites and 3D protein structures.

Q74. Proteostasis refers to:

A. DNA replication fidelity
B. Maintenance of protein homeostasis (folding, stability, degradation) ✅
C. Energy metabolism
D. RNA splicing

A/C/D: Not correct.
B: Proteostasis ensures functional proteome balance via chaperones and proteasomes.

Q75. The peptidome of a pathogen is important because:

A. It encodes DNA
B. Peptides can serve as antigens for vaccine development ✅
C. Peptides control transcription
D. Peptides cannot be detected

A/C/D: False.
B: Pathogen-derived peptides can trigger immune responses → used in vaccine design.

Proteomics MCQs — Part 4 (Q76–Q100)

Q76. Which technique is widely used for high-throughput protein identification?

A. Northern blot
B. PCR
C. LC-MS/MS ✅
D. Gel filtration

A/B: DNA/RNA methods.
C: LC-MS/MS is the backbone of proteomics for global protein ID.
D: Separates proteins but not high-throughput ID.

Q77. Which mass analyzer offers highest mass accuracy?

A. Quadrupole
B. TOF
C. Ion trap
D. Orbitrap ✅

A/C: Moderate accuracy.
B: TOF is good but less precise than Orbitrap.
D: Orbitrap offers ppm accuracy and ultra-high resolution.

Q78. Protein turnover rates can be studied using:

A. Western blot only
B. Pulse-chase experiments with isotopes ✅
C. SDS-PAGE alone
D. ELISA

A/C/D: Detect presence but not turnover rates.
B: Pulse-chase tracks synthesis and degradation dynamics.

Q79. Proteomic biomarkers are crucial for:

A. Astronomy
B. Disease diagnosis and prognosis ✅
C. Climate change studies
D. DNA sequencing

A/C/D: Not biomarker applications.
B: Proteomic biomarkers identify disease states, progression, or treatment response.

Q80. Hydrophobic interaction chromatography (HIC) separates proteins based on:

A. Charge
B. Hydrophobicity ✅
C. Size
D. Affinity tags

A: Ion exchange = charge.
B: HIC exploits hydrophobic patches on protein surfaces.
C: Size exclusion = size.
D: Affinity = specific tags.

Q81. Which is NOT a post-translational modification?

A. Phosphorylation
B. Glycosylation
C. Replication ✅
D. Ubiquitination

A/B/D: All PTMs.
C: Replication is a DNA process, not a protein modification.

Q82. Clinical proteomics focuses on:

A. Agricultural yields
B. Protein biomarkers for diagnosis/therapy ✅
C. Plant genome sequencing
D. Food processing

A/C/D: Not clinical applications.
B: Clinical proteomics applies to diagnostics, drug targets, personalized medicine.

Q83. Which proteomics technique uses isobaric chemical tags for multiplexing?

A. SILAC
B. iTRAQ / TMT ✅
C. Label-free LFQ
D. ELISA

A: Stable isotopes in vivo.
B: Isobaric tags allow multiplexed quantification in MS/MS.
C: No tags used.
D: Immunoassay.

Q84. Structural proteomics aims to:

A. Sequence RNA
B. Determine 3D structures of proteins and complexes ✅
C. Study only DNA-binding proteins
D. Quantify metabolites

A/D: Not proteomics.
B: Structural proteomics integrates X-ray, NMR, Cryo-EM, MS to study structures.
C: Too narrow.

Q85. Thermal proteome profiling (TPP) measures:

A. RNA folding
B. Protein stability shifts upon drug binding ✅
C. Protein phosphorylation
D. DNA replication

A/D: Not proteomics.
C: Different PTM analysis.
B: TPP identifies drug–protein targets by melting temperature shifts.

Q86. Which method is ideal for analyzing large protein complexes?

A. PCR
B. Blue Native PAGE + MS ✅
C. qPCR
D. SDS-PAGE

A/C: DNA-based.
D: Denatures complexes.
B: Native PAGE preserves complexes for MS analysis.

Q87. Which is a limitation of top-down proteomics?

A. Cannot detect PTMs
B. Low throughput and difficulty with large proteins ✅
C. Requires isotopic labeling always
D. No mass accuracy

A: Actually excels in PTM detection.
B: Large intact proteins are harder to analyze efficiently.
C: Labels optional.
D: Provides high accuracy.

Q88. SWATH-MS (DIA) differs from DDA because it:

A. Captures only one peptide at a time
B. Collects fragment ions for all peptides in wide windows ✅
C. Cannot quantify proteins
D. Needs isotope labels

A/C/D: Incorrect.
B: SWATH comprehensively records fragment data, later matched to spectral libraries.

Q89. NMR spectroscopy is most useful in proteomics for:

A. Gene sequencing
B. Studying protein structure and dynamics in solution ✅
C. RNA editing
D. ELISA development

A/C/D: Not NMR.
B: NMR provides structural and dynamic data for proteins in solution.

Q90. Which proteomic approach targets specific proteins with highest reproducibility?

A. Discovery proteomics
B. Targeted proteomics (SRM/MRM, PRM) ✅
C. Top-down proteomics
D. Protein microarrays

A: Broad, not targeted.
B: Targeted methods precisely quantify known proteins.
C/D: Not reproducible quant-only approaches.

Q91. Protein–ligand interactions can be studied by:

A. qPCR
B. Isothermal Titration Calorimetry (ITC) ✅
C. Southern blot
D. SDS-PAGE

A/C/D: DNA/protein separations, not ligand binding.
B: ITC directly measures heat of binding → affinity + thermodynamics.

Q92. The ubiquitin–proteasome system regulates:

A. RNA transcription
B. DNA repair only
C. Targeted degradation of proteins ✅
D. Protein secretion

A/D: Not main role.
B: Some repair proteins degraded, but not its definition.
C: UPS marks proteins with ubiquitin for proteasomal degradation.

Q93. Label-free proteomics can be challenged by:

A. Too many isotopes
B. Variability in sample prep and MS response ✅
C. Limited multiplexing
D. Antibody cross-reactivity

A/D: Not relevant.
C: Multiplexing is not labeling issue.
B: LFQ requires careful normalization to avoid bias.

Q94. The glycoproteome refers to:

A. All DNA methylation patterns
B. All glycosylated proteins in a system ✅
C. All glycolysis enzymes only
D. All lipid-bound proteins

A/D: Wrong.
C: Too narrow.
B: Glycoproteome = complete set of glycosylated proteins.

Q95. Protein chaperones function to:

A. Degrade proteins
B. Assist folding and prevent aggregation ✅
C. Modify DNA
D. Transport RNA

A: Proteasome does degradation.
B: Chaperones like Hsp70 stabilize folding intermediates.
C/D: Not chaperone roles.

Q96. Which proteomic method is best for absolute quantification?

A. Coomassie staining
B. AQUA peptides with isotopic internal standards ✅
C. Spectral counting
D. ELISA

A/C/D: Relative/semi-quantitative.
B: AQUA = stable-isotope labeled peptides for absolute copy number quantification.

Q97. Cross-linking MS (XL-MS) provides insights into:

A. RNA–DNA interactions
B. Protein–protein proximity and structural restraints ✅
C. Genetic mutations
D. Transcript splicing

A/C/D: Not correct.
B: XL-MS maps protein contacts for structural modeling.

Q98. Proteogenomics is especially useful for:

A. Protein folding
B. Improving genome annotation with proteomic evidence ✅
C. RNA sequencing
D. Metabolic flux

A/C/D: Other processes.
B: Proteogenomics aligns MS data with genome to refine coding sequences.

Q99. Which technology provides single-cell proteomics capability?

A. SDS-PAGE
B. Microfluidics + LC-MS/MS ✅
C. ELISA
D. Southern blot

A/C/D: Bulk or DNA/RNA methods.
B: Microfluidics enables protein analysis from individual cells.

Q100. Approximately how many proteins are encoded in the human genome (excluding isoforms)?

A. 100,000+
B. 50,000–70,000
C. ~20,000 ✅
D. ~200,000

A/D: Overestimates include isoforms/proteoforms.
B: Too high.
C: Human genome encodes ~20k proteins, though proteoforms vastly exceed this.

Proteomics mcqs for cbse board exams, proteomics mcqs for icse biology students, proteomics multiple choice questions for neet exam, proteomics mcqs with explanations for cuet entrance test, proteomics mcqs practice for csir net and gate, proteomics mcqs for dbt bet jrf preparation, proteomics mcqs with answers for usmle plab amc, proteomics practice questions for sat biology subject test, proteomics mcqs pdf for gre biology subject test, proteomics mcqs with solutions for bmat and imat