Q.1 Which technique is most commonly used to separate proteins based on their isoelectric point?
1D SDS-PAGE
Isoelectric Focusing (IEF)
Affinity Chromatography
Size Exclusion Chromatography
Explanation - Isoelectric focusing separates proteins by their pI; proteins migrate until they reach a pH equal to their isoelectric point. SDS-PAGE separates by molecular weight, while the other techniques rely on affinity or size.
Correct answer is: Isoelectric Focusing (IEF)
Q.2 In liquid chromatography-tandem mass spectrometry (LC-MS/MS), what is the purpose of the collision cell?
To ionize molecules in the gas phase
To fragment selected precursor ions for MS/MS analysis
To separate ions based on size
To desalinate the sample
Explanation - The collision cell (also called the collision-induced dissociation cell) induces fragmentation of selected precursor ions, generating product ions that are analyzed in the second MS stage.
Correct answer is: To fragment selected precursor ions for MS/MS analysis
Q.3 Which of the following best describes the term 'omics' in biology?
A method for sequencing DNA strands
A branch of science focused on large-scale data analysis of biological molecules
A type of laboratory instrument
A statistical technique for gene expression analysis
Explanation - The suffix '-omics' denotes a comprehensive, high-throughput study of a biological category, such as genomics, proteomics, or metabolomics.
Correct answer is: A branch of science focused on large-scale data analysis of biological molecules
Q.4 Which database is primarily used for storing protein–protein interaction data?
UniProt
PDB
STRING
KEGG
Explanation - STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) catalogs known and predicted protein–protein interactions. UniProt is a protein sequence database, PDB stores 3D structures, and KEGG is a pathway database.
Correct answer is: STRING
Q.5 In metabolomics, what does a 'feature' refer to?
A distinct metabolite identified by its m/z and retention time
A gene that encodes an enzyme
A specific cell type
An instrument setting
Explanation - Features are peaks detected in LC-MS data characterized by mass-to-charge ratio and retention time, representing potential metabolites.
Correct answer is: A distinct metabolite identified by its m/z and retention time
Q.6 Which algorithm is commonly used for deconvoluting isotopic distributions in mass spectrometry?
Dynamic Time Warping
Lagrange Interpolation
Deconvolution by Least Squares
Hidden Markov Models
Explanation - Least squares deconvolution is widely used to resolve overlapping isotopic patterns in high-resolution MS data.
Correct answer is: Deconvolution by Least Squares
Q.7 What does the term 'shotgun proteomics' mean?
Sequencing proteins from top to bottom
Digesting proteins into peptides and analyzing the mixture by LC-MS/MS
Using a single peptide to identify a protein
Isolating proteins by size exclusion chromatography
Explanation - Shotgun proteomics involves protease digestion of complex protein mixtures followed by LC-MS/MS, allowing simultaneous identification of many proteins.
Correct answer is: Digesting proteins into peptides and analyzing the mixture by LC-MS/MS
Q.8 Which of the following is NOT a typical objective of metabolomic profiling?
Biomarker discovery
Gene sequencing
Disease state characterization
Pathway elucidation
Explanation - Metabolomics focuses on small molecules; gene sequencing is part of genomics, not metabolomics.
Correct answer is: Gene sequencing
Q.9 In mass spectrometry, what does the term 'resolution' refer to?
The ability to distinguish between two ions with similar m/z values
The intensity of the detected ion peaks
The speed of data acquisition
The accuracy of mass measurement in Daltons
Explanation - Mass resolution indicates how well a spectrometer can separate close m/z signals; higher resolution allows detection of similar mass species.
Correct answer is: The ability to distinguish between two ions with similar m/z values
Q.10 Which software is widely used for quantitative proteomics data analysis?
Scaffold
Cytoscape
GROMACS
MATLAB
Explanation - Scaffold integrates peptide identification data from multiple search engines for protein inference and quantitation; Cytoscape visualizes networks, GROMACS simulates molecules, and MATLAB is a general programming platform.
Correct answer is: Scaffold
Q.11 What is the role of a 'label-free' quantitation method in proteomics?
It uses isotopic labels to quantify protein abundance
It relies on the intensity of MS signals without labeling
It requires fluorescent tags for detection
It measures protein abundance through antibody microarrays
Explanation - Label‑free quantitation compares MS signal intensities across runs; no chemical labels are attached to peptides.
Correct answer is: It relies on the intensity of MS signals without labeling
Q.12 Which analytical technique is best suited for detecting volatile metabolites in breath samples?
Gas Chromatography-Mass Spectrometry (GC-MS)
Liquid Chromatography-Mass Spectrometry (LC-MS)
Nuclear Magnetic Resonance (NMR) Spectroscopy
Capillary Electrophoresis (CE)
Explanation - GC-MS is ideal for volatile compounds; LC-MS is for nonvolatile, NMR provides structural info, and CE is used for charged analytes.
Correct answer is: Gas Chromatography-Mass Spectrometry (GC-MS)
Q.13 What is the purpose of a 'spectral library' in proteomics?
To store raw MS files for backup
To provide reference spectra for peptide identification
To catalogue genomic sequences
To manage instrument calibration schedules
Explanation - Spectral libraries contain experimentally acquired MS/MS spectra of known peptides, used for matching against observed spectra.
Correct answer is: To provide reference spectra for peptide identification
Q.14 Which of the following is a commonly used metabolite in cell culture media that serves as a carbon source?
Glucose
Lactate
Alanine
Citrate
Explanation - Glucose is the primary energy source for cultured cells; lactate is a byproduct, alanine is an amino acid, and citrate is part of the TCA cycle.
Correct answer is: Glucose
Q.15 In data preprocessing for metabolomics, what is the main purpose of 'normalization'?
To remove noise from raw signals
To adjust for systematic technical variation between samples
To convert m/z values to exact masses
To match metabolites to pathway databases
Explanation - Normalization scales data so that technical differences (e.g., injection volume) are minimized, allowing biological comparisons.
Correct answer is: To adjust for systematic technical variation between samples
Q.16 Which ionization technique is preferred for analyzing large intact proteins?
Electron Ionization (EI)
Matrix-Assisted Laser Desorption/Ionization (MALDI)
Electrospray Ionization (ESI)
Atmospheric Pressure Chemical Ionization (APCI)
Explanation - MALDI can ionize large biomolecules, including proteins, with minimal fragmentation, making it suitable for intact protein analysis.
Correct answer is: Matrix-Assisted Laser Desorption/Ionization (MALDI)
Q.17 Which computational approach is often used to integrate proteomics and metabolomics datasets?
Principal Component Analysis (PCA)
Phylogenetic tree construction
Sequence alignment
Monte Carlo simulation
Explanation - PCA reduces dimensionality and reveals patterns across heterogeneous omics data, facilitating integration and interpretation.
Correct answer is: Principal Component Analysis (PCA)
Q.18 What does 'LC–MS/MS' stand for?
Liquid Chromatography–Mass Spectrometry/Mass Spectrometry
Liquid Chromatography–Molecular Spectroscopy/Molecular Spectroscopy
Laser Capture Microdissection–Mass Spectrometry/Mass Spectrometry
Large Capillary – Methylsulfate Separation/Methylsulfate Separation
Explanation - LC–MS/MS denotes liquid chromatography coupled to tandem mass spectrometry for separating and analyzing molecules.
Correct answer is: Liquid Chromatography–Mass Spectrometry/Mass Spectrometry
Q.19 Which of the following is NOT a typical data type generated by LC-MS in metabolomics?
Peak intensity
Retention time
Gene sequence
Mass-to-charge ratio (m/z)
Explanation - LC-MS yields chromatographic and spectral data; gene sequences are produced by sequencing technologies.
Correct answer is: Gene sequence
Q.20 Why is a 'blank' sample run during an LC-MS experiment?
To calibrate the mass spectrometer
To detect contamination or carryover between runs
To test the sample's biological activity
To generate internal standards
Explanation - A blank (solvent only) identifies background signals and ensures that subsequent samples are not contaminated.
Correct answer is: To detect contamination or carryover between runs
Q.21 In proteomics, what is a 'unique peptide'?
A peptide that is found in all proteins
A peptide that maps to only one protein in the database
A peptide with the highest intensity
A synthetic peptide used as an internal standard
Explanation - Unique peptides allow confident protein identification because they are exclusive to a single protein.
Correct answer is: A peptide that maps to only one protein in the database
Q.22 Which of the following best describes the 'Metabolite Set Enrichment Analysis' (MSEA)?
A method to identify overrepresented gene sets in RNA‑seq data
A statistical approach to determine whether specific metabolite groups are significantly altered
A technique for measuring metabolite concentrations using NMR
An algorithm for clustering proteins by function
Explanation - MSEA evaluates whether predefined sets of metabolites (e.g., pathways) show coordinated changes across conditions.
Correct answer is: A statistical approach to determine whether specific metabolite groups are significantly altered
Q.23 Which of the following is a key challenge in integrating proteomics data with transcriptomics data?
Both datasets have the same dynamic range
Proteins and transcripts have identical half‑lives
Post‑translational modifications affect protein abundance independent of mRNA
Both are measured using the same instrumentation
Explanation - Proteins undergo modifications and degradation that are not directly reflected at the mRNA level, complicating integration.
Correct answer is: Post‑translational modifications affect protein abundance independent of mRNA
Q.24 Which ionization source is best suited for analyzing non‑polar lipids?
MALDI
APCI
ESI
EI
Explanation - Atmospheric Pressure Chemical Ionization efficiently ionizes relatively non‑polar molecules like lipids.
Correct answer is: APCI
Q.25 What is the main advantage of using a 'data‑dependent acquisition' (DDA) strategy in LC-MS/MS?
It captures all ions indiscriminately
It selectively fragments the most intense ions for MS/MS
It reduces the need for chromatographic separation
It eliminates the requirement for a mass spectrometer
Explanation - DDA monitors the full MS scan and triggers MS/MS on the top N most abundant precursor ions, enabling targeted fragmentation.
Correct answer is: It selectively fragments the most intense ions for MS/MS
Q.26 Which of the following is a commonly used internal standard for metabolomics LC-MS analysis?
Urea
Glucose
Leucine‑2,3,3,4,4,4‑d6
Actin
Explanation - Stable‑isotope labeled amino acids, such as deuterated leucine, are frequently spiked as internal standards for quantitation.
Correct answer is: Leucine‑2,3,3,4,4,4‑d6
Q.27 Which computational method is commonly used to predict protein–protein interaction interfaces?
Monte Carlo Tree Search
Molecular Docking
k‑Nearest Neighbors
Fourier Transform
Explanation - Docking simulates how two proteins may interact, predicting contact residues and binding affinity.
Correct answer is: Molecular Docking
Q.28 What does the term 'coverage' refer to in proteomics shotgun analysis?
The percentage of the genome sequenced
The fraction of a protein's sequence that is represented by identified peptides
The number of samples processed
The resolution of the mass spectrometer
Explanation - Coverage measures how much of a protein's amino acid sequence has been detected via peptides in the analysis.
Correct answer is: The fraction of a protein's sequence that is represented by identified peptides
Q.29 Which of these is NOT typically considered a metabolite class in metabolomics?
Amino acids
Lipids
Carbohydrates
Genes
Explanation - Genes are nucleic acids, not small metabolites measured in metabolomics studies.
Correct answer is: Genes
Q.30 What is a 'feature extraction' step in LC-MS metabolomics data processing?
Converting raw data to a visual plot
Identifying peaks and determining their m/z and retention time
Running the instrument calibration routine
Preparing the sample for injection
Explanation - Feature extraction isolates signal peaks from background noise, assigning each a precise m/z and retention time.
Correct answer is: Identifying peaks and determining their m/z and retention time
Q.31 Which of the following is a key advantage of using high‑resolution mass spectrometers (e.g., Orbitrap) in proteomics?
They are cheaper than low‑resolution instruments
They can separate ions with very close m/z values accurately
They require no chromatographic separation
They are immune to ion suppression effects
Explanation - High‑resolution instruments provide precise mass accuracy and resolving power, essential for distinguishing isobaric species.
Correct answer is: They can separate ions with very close m/z values accurately
Q.32 What does 'label‑based' quantitation in proteomics typically involve?
Using fluorescent tags on proteins
Adding stable isotope tags to peptides
Measuring only peptide intensities
Separating proteins by isoelectric point
Explanation - Label‑based methods (e.g., SILAC, TMT) attach isotopic labels to peptides, enabling multiplexed relative quantitation.
Correct answer is: Adding stable isotope tags to peptides
Q.33 Which of the following is a common data normalization method for LC‑MS metabolomics?
Log‑transform only
Median fold change normalization
Quantile normalization
Fourier filtering
Explanation - Quantile normalization forces identical distribution across samples, reducing technical variance.
Correct answer is: Quantile normalization
Q.34 Which of these is a major source of systematic error in LC‑MS metabolomics?
Biological variation
Instrument drift over time
Mass calibration
Data annotation errors
Explanation - Instrument drift (e.g., changes in sensitivity) can introduce systematic biases if not corrected.
Correct answer is: Instrument drift over time
Q.35 In mass spectrometry, the term 'ion trap' refers to:
A device that stores ions for a period before fragmentation
A chromatographic column used for ionization
A computational algorithm for spectral deconvolution
A method for desalting samples
Explanation - Ion traps confine ions in an electric field, allowing accumulation and selection for MS/MS.
Correct answer is: A device that stores ions for a period before fragmentation
Q.36 Which of the following is a feature of metabolomics that distinguishes it from transcriptomics?
Metabolites are directly encoded in DNA
Metabolites exhibit rapid turnover rates
Metabolomics requires less sample preparation
Metabolite analysis uses only gel electrophoresis
Explanation - Small molecules can change quickly in response to stimuli, unlike stable mRNA levels.
Correct answer is: Metabolites exhibit rapid turnover rates
Q.37 What is the typical unit for reporting protein abundance in label‑free proteomics?
Counts per million (CPM)
Spectral count
Peptide intensity in arbitrary units
Gene copy number
Explanation - Spectral counts represent the number of MS/MS spectra assigned to a protein, used as a proxy for abundance.
Correct answer is: Spectral count
Q.38 Which of the following best describes 'metabolic flux analysis'?
Measuring metabolite concentrations over time
Determining the rate of metabolic reactions using labeled substrates
Sequencing the genes encoding metabolic enzymes
Predicting protein folding pathways
Explanation - Metabolic flux analysis tracks how labeled atoms move through pathways, quantifying reaction rates.
Correct answer is: Determining the rate of metabolic reactions using labeled substrates
Q.39 What does 'peak‑to‑peak' refer to in electrophysiology?
The time interval between two consecutive action potentials
The difference in amplitude between the highest and lowest point of a signal
The ratio of two chromatographic peaks
A type of ionization technique
Explanation - Peak‑to‑peak amplitude measures signal strength, commonly used in signal processing.
Correct answer is: The difference in amplitude between the highest and lowest point of a signal
Q.40 Which of the following is NOT a type of post‑translational modification?
Phosphorylation
Acetylation
DNA methylation
Ubiquitination
Explanation - DNA methylation modifies nucleic acids, not proteins.
Correct answer is: DNA methylation
Q.41 In LC‑MS/MS, what is a 'precursor ion'?
An ion that results from fragmentation of a peptide
An ion that is selected for fragmentation in the second MS stage
An ion that is lost during ionization
An internal standard added to the sample
Explanation - The precursor ion is the intact ion selected in MS1 that will be fragmented in MS2.
Correct answer is: An ion that is selected for fragmentation in the second MS stage
Q.42 Which of the following is an advantage of using MALDI–TOF MS for peptide mass fingerprinting?
High resolution for small molecules
Fast acquisition time and minimal sample preparation
Ability to measure isoelectric points
Requirement for liquid chromatography
Explanation - MALDI‑TOF allows rapid analysis of peptide mixtures with little cleanup, ideal for fingerprinting.
Correct answer is: Fast acquisition time and minimal sample preparation
Q.43 Which of the following is a common data format for storing raw LC‑MS data?
FASTA
mzML
XML
CSV
Explanation - mzML is an open standard XML format for mass spectrometry data.
Correct answer is: mzML
Q.44 What is a 'false discovery rate' (FDR) in proteomics?
The probability that a peptide identification is a false positive
The ratio of true positives to false negatives
The rate of sample loss during preparation
The frequency of instrument downtime
Explanation - FDR controls the expected proportion of incorrectly identified peptides in a dataset.
Correct answer is: The probability that a peptide identification is a false positive
Q.45 Which of the following best defines a 'metabolite biomarker'?
A molecule that directly causes disease
A metabolite whose levels correlate with a disease state
A protein that is overexpressed in cancer
A DNA sequence variation linked to phenotype
Explanation - Metabolite biomarkers are measurable metabolites that indicate health or disease status.
Correct answer is: A metabolite whose levels correlate with a disease state
Q.46 Which computational technique is often used to align multiple LC‑MS runs?
Dynamic Time Warping (DTW)
Fourier Transform
Principal Component Analysis
Maximum Likelihood Estimation
Explanation - DTW aligns retention times across runs, accounting for chromatographic drift.
Correct answer is: Dynamic Time Warping (DTW)
Q.47 In metabolomics, what does 'untargeted analysis' mean?
Analyzing only known metabolites
Using a predefined list of metabolites
Collecting data without prior selection of analytes
Targeting specific protein–protein interactions
Explanation - Untargeted metabolomics aims to detect as many metabolites as possible, not limited to a preset list.
Correct answer is: Collecting data without prior selection of analytes
Q.48 Which of the following is a common ionization mode for detecting acidic metabolites in LC‑MS?
Positive ion mode
Negative ion mode
Neutral mode
Both positive and negative simultaneously
Explanation - Acidic metabolites ionize efficiently in negative mode, forming [M-H]⁻ ions.
Correct answer is: Negative ion mode
Q.49 What is the main purpose of using a 'lock‑mass' in mass spectrometry?
To calibrate the retention time scale
To provide a constant reference ion for mass accuracy
To act as an internal standard for quantitation
To improve chromatographic separation
Explanation - Lock‑mass ions are injected continuously to correct mass drift during a run.
Correct answer is: To provide a constant reference ion for mass accuracy
Q.50 Which of the following best describes 'data‑independent acquisition' (DIA) in LC‑MS/MS?
Acquiring MS/MS spectra for every possible precursor ion simultaneously
Fragmenting only the top N most intense precursors
Using only a single ion for quantitation
Acquiring data in real‑time without storage
Explanation - DIA collects MS/MS data for all ions in a predefined m/z window, enabling comprehensive coverage.
Correct answer is: Acquiring MS/MS spectra for every possible precursor ion simultaneously
Q.51 Which of the following is a commonly used bioinformatics tool for pathway enrichment analysis in metabolomics?
ReactomePA
BLAST
PhyML
Clustal Omega
Explanation - ReactomePA provides pathway enrichment for metabolomic datasets, mapping metabolites to curated pathways.
Correct answer is: ReactomePA
Q.52 In proteomics, what is 'protein inference'?
Predicting protein structure from amino acid sequence
Assigning identified peptides to their parent proteins
Estimating protein expression levels from RNA‑seq data
Designing primers for protein amplification
Explanation - Protein inference determines which proteins are present based on observed peptide data.
Correct answer is: Assigning identified peptides to their parent proteins
Q.53 Which of the following best defines 'isobaric labeling' in proteomics?
Labeling peptides with isotopes that do not alter mass
Labeling peptides with isotopes that change mass by the same amount for different samples
Labeling proteins based on charge state
Labeling proteins by their isoelectric points
Explanation - Isobaric tags (e.g., TMT, iTRAQ) produce identical mass ions but release distinct reporter ions upon fragmentation.
Correct answer is: Labeling peptides with isotopes that change mass by the same amount for different samples
Q.54 What is the primary function of a 'chromatographic gradient' in LC‑MS?
To maintain a constant temperature
To vary solvent composition to improve analyte separation
To calibrate the mass spectrometer
To filter out salts from the sample
Explanation - A gradient increases elution strength over time, helping separate compounds with diverse polarities.
Correct answer is: To vary solvent composition to improve analyte separation
Q.55 Which of these is an example of a 'biologically relevant metabolite' in the human plasma?
Glucose
Sodium chloride
Caffeine
Hydrogen peroxide
Explanation - Glucose is a central metabolite in human metabolism; the others are salts, a drug, or a reactive oxygen species.
Correct answer is: Glucose
Q.56 What is the main advantage of using a 'nanoflow LC' system for proteomic analysis?
Higher flow rates reduce analysis time
Reduced sample consumption and increased sensitivity
Simpler instrumentation
Lower cost of operation
Explanation - Nanoflow LC achieves better ionization efficiency and lower sample usage, improving detection limits.
Correct answer is: Reduced sample consumption and increased sensitivity
Q.57 Which of the following best describes 'metabolite annotation' in metabolomics?
Assigning metabolites to genomic loci
Identifying the chemical identity of detected features
Labeling metabolites with isotopes
Predicting protein‑protein interactions
Explanation - Annotation matches observed m/z and retention times to known metabolite databases.
Correct answer is: Identifying the chemical identity of detected features
Q.58 Which computational approach is commonly used for clustering metabolomic data?
Hierarchical clustering
Random Forest
K‑means clustering
Support Vector Machine
Explanation - Hierarchical clustering groups samples based on similarity, often visualized as a dendrogram.
Correct answer is: Hierarchical clustering
Q.59 In a proteomics experiment, what does a 'spectral library search' entail?
Searching raw spectra against a database of known peptide sequences
Searching spectra against a library of experimentally derived spectra
Searching spectra against DNA sequences
Searching spectra against a set of protein structures
Explanation - Spectral library search compares acquired spectra to a reference library, often yielding higher identification confidence.
Correct answer is: Searching spectra against a library of experimentally derived spectra
Q.60 Which of the following is a key feature of 'data‑dependent acquisition' (DDA) that can limit quantitative accuracy?
The use of stable‑isotope labels
Sampling bias towards the most abundant precursors
High mass resolution
Real‑time data processing
Explanation - DDA preferentially fragments abundant ions, potentially missing low‑abundance peptides.
Correct answer is: Sampling bias towards the most abundant precursors
Q.61 Which of the following is NOT a common data output from an LC‑MS run?
Raw data files (e.g., mzML)
Processed peak tables
Spectral libraries
Protein sequences in FASTA format
Explanation - FASTA files contain nucleotide or protein sequences, not directly generated by LC‑MS.
Correct answer is: Protein sequences in FASTA format
Q.62 What does 'molecular networking' involve in metabolomics?
Connecting metabolites based on shared biosynthetic genes
Visualizing relationships between metabolites using MS/MS similarity
Linking proteins to metabolites via protein–protein interaction networks
Mapping metabolite transport across membranes
Explanation - Molecular networking groups spectra by similarity, revealing structural relationships among metabolites.
Correct answer is: Visualizing relationships between metabolites using MS/MS similarity
Q.63 Which of the following best describes the 'chromatographic peak width'?
The time span between the first and last eluting compound
The full width at half maximum (FWHM) of a chromatographic peak
The width of the column used in chromatography
The width of the ion source
Explanation - Peak width indicates resolution; narrower peaks imply better separation.
Correct answer is: The full width at half maximum (FWHM) of a chromatographic peak
Q.64 Which of the following is a typical application of proteogenomics?
Integrating proteomics data with gene annotation to improve genome assemblies
Sequencing the entire proteome
Mapping metabolic pathways
Detecting DNA methylation patterns
Explanation - Proteogenomics uses proteomics to validate and refine gene models.
Correct answer is: Integrating proteomics data with gene annotation to improve genome assemblies
Q.65 Which of the following best explains 'isotopic labeling' in metabolomics?
Using heavy isotope–enriched substrates to trace metabolic fluxes
Adding fluorescent tags to metabolites
Replacing a metabolite with its synthetic counterpart
Separating metabolites based on charge
Explanation - Isotopic labeling tracks how atoms are incorporated into metabolites, revealing pathway activity.
Correct answer is: Using heavy isotope–enriched substrates to trace metabolic fluxes
Q.66 What is a 'protein‑specific peptide'?
A peptide that is shared by multiple proteins
A peptide that maps uniquely to a single protein
A peptide used for immunoprecipitation
A peptide with a post‑translational modification
Explanation - Protein‑specific peptides serve as reliable identifiers for that protein in mass spectrometry.
Correct answer is: A peptide that maps uniquely to a single protein
Q.67 Which of the following is a main challenge in quantitative metabolomics?
Limited number of detectable metabolites
Inability to separate compounds by chromatography
High variability in ion suppression effects
Absence of mass spectrometry standards
Explanation - Matrix effects can cause inconsistent ionization, affecting quantitation accuracy.
Correct answer is: High variability in ion suppression effects
Q.68 In LC‑MS, what does the 'signal‑to‑noise ratio' (SNR) indicate?
The ratio of ion intensity to background noise level
The ratio of m/z to retention time
The ratio of data points to total scans
The ratio of protein to metabolite abundance
Explanation - A high SNR means the analyte peak stands out clearly from the noise, improving detection confidence.
Correct answer is: The ratio of ion intensity to background noise level
Q.69 Which of the following is a type of post‑translational modification that adds a phosphate group?
Glycosylation
Phosphorylation
Methylation
Acetylation
Explanation - Phosphorylation is the covalent addition of a phosphate group to proteins, often regulating function.
Correct answer is: Phosphorylation
Q.70 Which of these is an example of a 'metabolite'?
DNA polymerase
Adenosine triphosphate (ATP)
Hemoglobin
Myosin
Explanation - ATP is a small molecule metabolite involved in energy transfer, whereas the others are proteins.
Correct answer is: Adenosine triphosphate (ATP)
Q.71 What is the function of a 'stand‑by' mode in a mass spectrometer?
To continuously acquire data without user input
To prepare the instrument for the next run by calibrating and stabilizing
To store raw data for later analysis
To automatically annotate spectra
Explanation - Stand‑by mode keeps the system ready, performing maintenance tasks such as tuning.
Correct answer is: To prepare the instrument for the next run by calibrating and stabilizing
Q.72 Which of the following best describes 'label‑free spectral counting'?
Counting spectra matched to a protein without using labeled standards
Using labeled peptides to determine spectral counts
Counting spectral peaks in a chromatogram
Using spectral counts for pathway analysis
Explanation - Label‑free spectral counting estimates protein abundance by tallying MS/MS spectra assigned to it.
Correct answer is: Counting spectra matched to a protein without using labeled standards
Q.73 Which of the following best defines a 'chromatographic retention time shift'?
A change in the mass of an analyte
A difference in the time an analyte elutes between runs
A shift in the detector baseline
A variation in ion source temperature
Explanation - Retention time shift indicates chromatographic variability, requiring alignment.
Correct answer is: A difference in the time an analyte elutes between runs
Q.74 In metabolomics, why is 'sample derivatization' sometimes performed?
To increase the mass of the metabolite
To improve chromatographic properties and ionization efficiency
To reduce the number of peaks in the spectrum
To eliminate the need for chromatography
Explanation - Derivatization modifies polar metabolites, making them more amenable to separation and detection.
Correct answer is: To improve chromatographic properties and ionization efficiency
Q.75 Which of the following is a major benefit of using 'Orbitrap' mass analyzers?
Very fast scanning speed
High resolution and mass accuracy
Low cost
No need for ionization source
Explanation - Orbitraps deliver high resolution and accurate mass measurements, crucial for complex mixtures.
Correct answer is: High resolution and mass accuracy
Q.76 Which of the following is a typical outcome of a 'protein–protein interaction (PPI) network' analysis?
Identification of potential drug targets
Sequencing of the entire proteome
Prediction of metabolite structures
Determination of DNA methylation patterns
Explanation - PPI networks highlight key hubs that can be targeted therapeutically.
Correct answer is: Identification of potential drug targets
Q.77 What does the term 'fold change' refer to in quantitative proteomics?
The difference between two protein lengths
The ratio of protein abundance between two conditions
The number of proteins detected in a run
The difference between two retention times
Explanation - Fold change quantifies up‑ or down‑regulation of a protein across conditions.
Correct answer is: The ratio of protein abundance between two conditions
Q.78 Which of the following best describes 'label‑based quantitation' using TMT reagents?
Each sample is labeled with a different isotopic tag and combined before LC‑MS/MS
All samples are analyzed separately without labeling
A single internal standard is added to all samples
Protein levels are inferred from mRNA data
Explanation - TMT reagents allow multiplexing by labeling peptides with distinct reporter ions.
Correct answer is: Each sample is labeled with a different isotopic tag and combined before LC‑MS/MS
Q.79 Which of the following is a primary advantage of using 'gas chromatography' (GC) in metabolomics?
It can analyze non‑volatile, polar metabolites directly
It offers high-resolution mass analysis for all metabolites
It can separate volatile metabolites with high reproducibility
It requires no derivatization
Explanation - GC is ideal for volatile compounds; non‑volatiles require derivatization.
Correct answer is: It can separate volatile metabolites with high reproducibility
Q.80 What is a key feature of a 'data‑independent acquisition' (DIA) spectral library?
It contains only experimental spectra
It includes predicted spectra for all possible peptides
It excludes low‑confidence identifications
It is generated by a single instrument run
Explanation - DIA libraries are built from high‑quality experimental spectra used for peptide identification.
Correct answer is: It contains only experimental spectra
Q.81 In proteomics, what does 'protein‑level quantitation' aim to achieve?
Determine the number of proteins present in a sample
Calculate the relative abundance of proteins between samples
Identify the gene responsible for a protein
Measure the molecular weight of a protein
Explanation - Protein‑level quantitation compares protein amounts across conditions or time points.
Correct answer is: Calculate the relative abundance of proteins between samples
Q.82 Which of the following is a characteristic of 'targeted metabolomics'?
Analysis of all detectable metabolites in a sample
Quantification of a predefined list of metabolites
No chromatographic separation
Use of only unlabeled internal standards
Explanation - Targeted metabolomics focuses on specific analytes, improving sensitivity and precision.
Correct answer is: Quantification of a predefined list of metabolites
Q.83 Which of the following best describes 'protein‑based bioinformatics'?
Predicting the structure of DNA sequences
Analyzing protein sequences and structures computationally
Identifying metabolites in LC‑MS data
Mapping metabolic pathways
Explanation - Protein bioinformatics deals with computational analysis of amino acid sequences and protein models.
Correct answer is: Analyzing protein sequences and structures computationally
Q.84 Which of the following best describes 'spectral count normalization' in proteomics?
Adjusting spectral counts by the number of peptides per protein
Converting spectral counts to log‑scale
Normalizing counts against a housekeeping protein
Dividing spectral counts by the total number of spectra acquired
Explanation - Normalization accounts for varying total spectra between runs, enabling fair comparison.
Correct answer is: Dividing spectral counts by the total number of spectra acquired
Q.85 Which of the following is an example of a 'bioinformatics pipeline' for proteomics?
Raw data acquisition → Peak extraction → Database search → Protein inference → Quantitation
Sample preparation → Chromatography → Mass spectrometry → Data annotation
Gene sequencing → Variant calling → Functional annotation
Metabolite extraction → NMR analysis → Pathway mapping
Explanation - This pipeline outlines the computational steps from raw MS data to protein-level results.
Correct answer is: Raw data acquisition → Peak extraction → Database search → Protein inference → Quantitation
Q.86 Which of the following is a common strategy to mitigate ion suppression in LC‑MS metabolomics?
Using a higher flow rate in chromatography
Adding more sample to the injection
Using a larger injection volume
Optimizing chromatographic separation and using matrix‑matched calibration
Explanation - Improved separation reduces co‑elution, while matrix matching corrects for ion suppression.
Correct answer is: Optimizing chromatographic separation and using matrix‑matched calibration
Q.87 What does the 'mass defect' of a metabolite refer to?
The difference between the exact mass and the nominal mass of an ion
The mass difference between two isotopic peaks
The mass of a metabolite after ionization
The mass of a metabolite plus its isotopic label
Explanation - Mass defect is the fractional part of a mass that differs from an integer, useful in isotope analysis.
Correct answer is: The difference between the exact mass and the nominal mass of an ion
Q.88 Which of the following is a key consideration when choosing a database for protein identification?
Database size does not affect search time
Including decoy sequences for FDR estimation
Using only a single species database
Avoiding any post‑translational modifications in the database
Explanation - Decoy sequences allow estimation of false discovery rates during database searching.
Correct answer is: Including decoy sequences for FDR estimation
Q.89 What is a 'metabolite signature' in the context of disease diagnostics?
A unique protein sequence signature
A pattern of metabolite levels that distinguishes disease from healthy state
A set of DNA mutations
A specific peptide fragment
Explanation - Metabolite signatures are used as biomarkers for diagnosing or monitoring diseases.
Correct answer is: A pattern of metabolite levels that distinguishes disease from healthy state
Q.90 Which of the following best describes 'chromatographic peak picking'?
Selecting the most intense ion from a spectrum
Identifying and quantifying chromatographic peaks from raw data
Choosing the best column for separation
Determining the retention time of a standard
Explanation - Peak picking isolates signals from background noise for further analysis.
Correct answer is: Identifying and quantifying chromatographic peaks from raw data
Q.91 Which of the following is NOT a common step in preparing a sample for LC‑MS analysis of metabolites?
Protein precipitation
Derivatization of polar compounds
Filtration to remove particulates
Direct injection without any treatment
Explanation - Most metabolite samples require cleanup steps to avoid contamination and improve detection.
Correct answer is: Direct injection without any treatment
Q.92 Which of the following best explains 'ion suppression'?
A phenomenon where low‑molecular‑weight ions are preferentially detected
A reduction in ionization efficiency due to matrix effects
An increase in ion fragmentation efficiency
A method of enhancing signal intensity
Explanation - Ion suppression occurs when co‑eluting substances reduce the signal of analytes.
Correct answer is: A reduction in ionization efficiency due to matrix effects
Q.93 Which of the following best describes 'orthogonal separation' in LC‑MS workflows?
Using two chromatographic dimensions with different selectivities
Applying the same separation method twice
Using only mass spectrometry without chromatography
Separating ions based solely on charge state
Explanation - Orthogonal separations (e.g., RPLC followed by HILIC) improve peak capacity.
Correct answer is: Using two chromatographic dimensions with different selectivities
Q.94 In mass spectrometry, what is a 'charge state distribution'?
The distribution of ions across different m/z values
The ratio of positive to negative ions
The distribution of ion charge states (e.g., +2, +3) in a spectrum
The variation in ionization efficiency across analytes
Explanation - Proteins and peptides can carry multiple charges; the distribution affects mass spectra interpretation.
Correct answer is: The distribution of ion charge states (e.g., +2, +3) in a spectrum
Q.95 Which of the following best describes 'mass‑resolved deconvolution' in proteomics?
Separating peptides by mass before LC
Resolving overlapping isotope patterns to determine monoisotopic mass
Converting mass spectra to chromatograms
Annotating metabolites with pathway information
Explanation - Deconvolution corrects for overlapping isotopes, providing accurate mass assignments.
Correct answer is: Resolving overlapping isotope patterns to determine monoisotopic mass
Q.96 Which of the following is an example of a 'post‑translational modification' that can be detected by LC‑MS?
DNA replication
Protein phosphorylation
RNA splicing
Cell division
Explanation - LC‑MS can identify modified peptides, revealing post‑translational changes such as phosphorylation.
Correct answer is: Protein phosphorylation
Q.97 What is the purpose of a 'blank injection' in an LC‑MS workflow?
To calibrate the mass spectrometer
To clean the column and assess background signals
To provide an internal standard
To test the instrument's sensitivity
Explanation - Blank injections identify carryover and baseline noise, ensuring data quality.
Correct answer is: To clean the column and assess background signals
Q.98 Which of the following best describes 'high‑throughput proteomics'?
Analyzing a small number of proteins in detail
Rapidly analyzing large numbers of proteins across many samples
Sequencing proteins by mass spectrometry alone
Using only single‑cell proteomics
Explanation - High‑throughput proteomics emphasizes speed, scalability, and automation.
Correct answer is: Rapidly analyzing large numbers of proteins across many samples
Q.99 Which of the following is a typical preprocessing step for LC‑MS metabolomic data?
Converting data to FASTA format
Background subtraction and baseline correction
Amplifying DNA fragments
Performing protein sequencing
Explanation - Preprocessing cleans the data, removing noise before downstream analysis.
Correct answer is: Background subtraction and baseline correction
Q.100 What is the main advantage of using 'ion mobility spectrometry' (IMS) in conjunction with MS?
It separates ions based on size and shape, adding an orthogonal dimension
It eliminates the need for chromatography
It provides direct structural information without fragmentation
It reduces the cost of instrumentation
Explanation - IMS separates ions by drift time, enhancing resolution and enabling isomer discrimination.
Correct answer is: It separates ions based on size and shape, adding an orthogonal dimension
Q.101 In metabolomics, which of the following best defines a 'feature table'?
A list of proteins identified in a proteomic experiment
A matrix of metabolite intensities across samples
A database of DNA sequences
A schematic of metabolic pathways
Explanation - A feature table contains quantified feature values (m/z, RT, intensity) for each sample.
Correct answer is: A matrix of metabolite intensities across samples
Q.102 Which of the following best describes the 'limit of detection' (LOD) in mass spectrometry?
The lowest concentration of an analyte that can be reliably quantified
The highest concentration of an analyte that can be measured
The time required to detect an analyte
The number of ions generated in the ion source
Explanation - LOD represents the lowest detectable signal above background noise.
Correct answer is: The lowest concentration of an analyte that can be reliably quantified
Q.103 Which of the following is a common use for 'Principal Component Analysis' (PCA) in proteomics?
To predict protein structures
To reduce dimensionality and identify sample clustering
To identify post‑translational modifications
To quantify peptide concentrations
Explanation - PCA transforms data into orthogonal components, revealing patterns and outliers.
Correct answer is: To reduce dimensionality and identify sample clustering
Q.104 What is a 'feature extraction' step in LC‑MS metabolomics data processing?
Identifying peaks and determining their m/z and retention time
Annotating metabolites with pathway information
Preparing samples for injection
Converting spectra to images
Explanation - Feature extraction isolates analyte signals from raw data for downstream analysis.
Correct answer is: Identifying peaks and determining their m/z and retention time
Q.105 Which of the following best describes a 'mass defect filter'?
Filtering ions based on their mass defect to isolate a chemical class
Filtering spectra based on signal intensity
Filtering chromatographic peaks by retention time
Filtering peptides by charge state
Explanation - Mass defect filters select ions with a specific mass defect, useful for targeting certain metabolite classes.
Correct answer is: Filtering ions based on their mass defect to isolate a chemical class
Q.106 Which of the following is a typical application of metabolite profiling in plant biology?
Determining plant DNA sequence variation
Analyzing leaf metabolite changes in response to stress
Mapping protein–protein interactions
Sequencing the entire proteome
Explanation - Metabolite profiling reveals biochemical responses of plants to environmental stimuli.
Correct answer is: Analyzing leaf metabolite changes in response to stress