Proteome overview MCQs With Answer

Proteome overview MCQs With Answer

This concise quiz collection is designed for M.Pharm students to strengthen core concepts in proteomics and its computational analysis. Covering techniques such as 2D-PAGE, LC-MS/MS, top-down versus bottom-up strategies, quantitative labeling (SILAC, iTRAQ/TMT), and bioinformatics tools (UniProt, PRIDE, database search engines), these MCQs focus on practical and theoretical aspects relevant to drug discovery and biomarker research. Questions emphasize experimental design, mass spectrometry principles, peptide identification, post-translational modification analysis, and data interpretation metrics like false discovery rate. Each question is followed by clear answer keys to facilitate rapid self-assessment and deeper study of proteome-level investigations.

Q1. What is the best definition of the term “proteome”?

• The complete set of RNA transcripts produced by a cell or tissue
• The complete set of metabolic reactions in an organism
• The entire complement of proteins expressed by a cell, tissue or organism at a given time under specific conditions
• The total genomic DNA sequence of an organism

Correct Answer: The entire complement of proteins expressed by a cell, tissue or organism at a given time under specific conditions

Q2. Which technique is most commonly used for high-throughput identification of proteins in complex mixtures?

• Western blotting
• Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)
• Immunohistochemistry
• Sanger sequencing

Correct Answer: Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)

Q3. In bottom-up proteomics, what is the primary sample processing step before MS analysis?

• Whole protein analysis without digestion
• Chemical crosslinking of intact proteins
• Proteolytic digestion (commonly with trypsin) into peptides
• Direct genomic amplification of protein-coding genes

Correct Answer: Proteolytic digestion (commonly with trypsin) into peptides

Q4. Which ionization method is particularly well-suited for coupling with LC and generating multiply charged peptide ions?

• MALDI (Matrix-Assisted Laser Desorption/Ionization)
• Electrospray Ionization (ESI)
• Electron Impact ionization
• Fast Atom Bombardment

Correct Answer: Electrospray Ionization (ESI)

Q5. What does the term “shotgun proteomics” refer to?

• Analysis of intact proteins by top-down MS
• Targeted measurement of a single protein using immunoassays
• Untargeted LC-MS/MS analysis of complex peptide mixtures derived from proteolytic digestion
• Use of MALDI imaging to map proteins in tissues

Correct Answer: Untargeted LC-MS/MS analysis of complex peptide mixtures derived from proteolytic digestion

Q6. Which fragmentation ion series is most useful for peptide sequence interpretation in CID/HCD tandem MS spectra?

• a and x ions
• b and y ions
• c and z ions
• m and n ions

Correct Answer: b and y ions

Q7. What is the purpose of using a decoy database when performing MS/MS database searches?

• To increase search speed by reducing database size
• To provide internal calibration masses for the instrument
• To estimate false discovery rate (FDR) by measuring matches to reversed or randomized sequences
• To store post-translational modification annotations

Correct Answer: To estimate false discovery rate (FDR) by measuring matches to reversed or randomized sequences

Q8. Which quantitative proteomics strategy uses metabolic incorporation of heavy isotopes into proteins during cell culture?

• iTRAQ labeling
• TMT labeling
• SILAC (Stable Isotope Labeling by Amino acids in Cell culture)
• Label-free spectral counting

Correct Answer: SILAC (Stable Isotope Labeling by Amino acids in Cell culture)

Q9. In isobaric labeling methods (iTRAQ/TMT), how are relative abundances of peptides determined?

• By precursor ion m/z differences in MS1
• By reporter ion intensities measured in MS2 or MS3 spectra
• By retention time shifts during LC
• By absolute peptide masses without fragmentation

Correct Answer: By reporter ion intensities measured in MS2 or MS3 spectra

Q10. Which database is a primary curated source for protein sequence and functional annotation widely used in proteomics?

• PRIDE
• KEGG
• UniProt
• Gene Ontology (GO)

Correct Answer: UniProt

Q11. What major limitation of 2D-PAGE affects its utility for comprehensive proteome profiling?

• High sensitivity for very low-abundance proteins
• Inability to separate proteins by isoelectric point
• Poor resolution of very hydrophobic and extreme molecular weight proteins, and limited dynamic range
• It provides sequence-level identification directly

Correct Answer: Poor resolution of very hydrophobic and extreme molecular weight proteins, and limited dynamic range

Q12. Which MS analyzer is known for very high mass accuracy and resolving power, commonly used in proteomics?

• Quadrupole
• Ion trap
• Orbitrap
• Magnetic sector

Correct Answer: Orbitrap

Q13. What is a peptide “missed cleavage” and why is it important in database searches?

• A peptide that failed to ionize and thus is missing from MS data
• A peptide resulting from non-enzymatic cleavage during storage
• An instance where the protease did not cleave at an expected site, producing longer peptides that must be allowed for in search parameters
• An artifact from MALDI ion suppression

Correct Answer: An instance where the protease did not cleave at an expected site, producing longer peptides that must be allowed for in search parameters

Q14. Which strategy is commonly used to enrich phosphorylated peptides prior to LC-MS/MS analysis?

• Size-exclusion chromatography
• Immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO2) enrichment
• Gel filtration without affinity steps
• Reverse-phase desalting only

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

Q15. What does “label-free quantitation” in proteomics usually rely on?

• Stable isotope internal standards
• Comparison of reporter ion intensities
• Comparing MS1 peak intensities or spectral counting across runs with normalization
• Chemical derivatization with isotopic tags

Correct Answer: Comparing MS1 peak intensities or spectral counting across runs with normalization

Q16. Which repository is specifically designed for archiving and sharing raw and processed proteomics data?

• PubMed
• PRIDE (Proteomics Identifications Database)
• Reactome
• RefSeq

Correct Answer: PRIDE (Proteomics Identifications Database)

Q17. In tandem mass spectrometry, what is the significance of the term “MS/MS”?

• Sequencing of DNA and RNA simultaneously
• Two stages of mass selection and fragmentation: precursor ion selection (MS1) followed by fragmentation and analysis of product ions (MS2)
• Measurement of mass twice to improve accuracy
• Dual ionization methods used sequentially

Correct Answer: Two stages of mass selection and fragmentation: precursor ion selection (MS1) followed by fragmentation and analysis of product ions (MS2)

Q18. Which metric is commonly used to control confidence in peptide-spectrum matches (PSMs) and protein identifications?

• Ion injection time
• False discovery rate (FDR)
• Retention time only
• pH of the mobile phase

Correct Answer: False discovery rate (FDR)

Q19. What is the principal advantage of top-down proteomics compared with bottom-up approaches?

• Easier analysis of very large proteomes with no instrumentation limits
• Direct analysis of intact proteins allowing characterization of proteoforms and combinatorial post-translational modifications
• Requires no high-resolution mass spectrometers
• No need for chromatographic separation

Correct Answer: Direct analysis of intact proteins allowing characterization of proteoforms and combinatorial post-translational modifications

Q20. Which factor most limits the depth of proteome coverage in a typical LC-MS/MS experiment?

• The number of tryptic cleavage sites in proteins
• The dynamic range of protein abundances in the sample combined with instrument sensitivity and duty cycle
• The electrical power available to the mass spectrometer
• The color of the sample solvent

Correct Answer: The dynamic range of protein abundances in the sample combined with instrument sensitivity and duty cycle

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