Protein Separation Techniques in Proteomics

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Questions and Answers

What does a qualitative ELISA determine?

  • The exact concentration of an antibody in a sample
  • The titer of a particular antibody
  • The presence of multiple analytes simultaneously
  • The presence or absence of an antigen or antibody (correct)

In a multiplex immunoassay, how is the specific identification of analytes achieved?

  • Through the use of a single laser to measure fluorescence intensity only
  • By mixing all samples and measuring the total fluorescence together
  • By associating different analytes with unique bead regions that have distinct spectral signatures (correct)
  • By using a single type of fluorescent dye for all beads

What role does streptavidin-phycoerythrin (PE) play in the multiplex immunoassay process?

  • It labels the beads to identify various analytes
  • It washes away unbound materials from the beads
  • It acts as a reporter to indicate the magnitude of the analyte binding (correct)
  • It quantifies the concentration of antibodies in the sample

What feature of a bead-based multiplex immunoassay allows for the detection of up to 100 analytes at once?

<p>Color-coded microspheres with distinct spectral signatures (C)</p> Signup and view all the answers

What does the titer in a quantitative ELISA represent?

<p>The dilution factor at which a positive reaction is obtained (C)</p> Signup and view all the answers

What is the primary function of the enzyme-linked immunosorbent assay (ELISA)?

<p>To measure antibodies, antigens, proteins, and glycoproteins (B)</p> Signup and view all the answers

In the workflow of proteomics, which step immediately follows the sample stage?

<p>Extraction (B)</p> Signup and view all the answers

Which of the following is not a type of ELISA?

<p>Mass spectrometry ELISA (D)</p> Signup and view all the answers

How do the results of an ELISA test typically present?

<p>As a quantifiable color change (C)</p> Signup and view all the answers

What is the reason for using 96 well plates in ELISA assays?

<p>To facilitate the measurement of multiple samples simultaneously (C)</p> Signup and view all the answers

Which technique is considered a high-throughput method in proteomics?

<p>Mass spectrometry-based proteomics (C)</p> Signup and view all the answers

What is the role of the substrate in an ELISA assay?

<p>To react with the enzyme, producing a detectable product (D)</p> Signup and view all the answers

Which of these components is meant to specifically recognize the antigen during an ELISA?

<p>The first specific antibody (B)</p> Signup and view all the answers

What is the primary purpose of measuring retention time in liquid chromatography?

<p>To assess the time taken for a solute to pass through the chromatography column (C)</p> Signup and view all the answers

What is NOT an advantage of liquid chromatography?

<p>High running costs for every analysis (A)</p> Signup and view all the answers

In gas chromatography, what is the role of the mobile phase?

<p>To facilitate the separation of analytes in the gas phase (B)</p> Signup and view all the answers

Which gas is most commonly used as a mobile phase in gas chromatography due to its low molecular weight?

<p>Helium (B)</p> Signup and view all the answers

What technique is used to identify the amount and type of chemicals in a sample through the analysis of ions?

<p>Mass Spectrometry (B)</p> Signup and view all the answers

Which of the following is NOT a characteristic of the stationary phase in gas chromatography?

<p>It vaporizes samples during injection (D)</p> Signup and view all the answers

What is measured in mass spectrometry to help identify chemicals in a sample?

<p>Mass-to-charge ratio and abundance of ions (B)</p> Signup and view all the answers

Which technique would most likely be used for analyzing small molecular weight compounds?

<p>Gas chromatography (B)</p> Signup and view all the answers

What is the formula for calculating the m/z ratio?

<p>Molecular weight / Charge (D)</p> Signup and view all the answers

Which ionization method forms singly charged ions?

<p>MALDI (Matrix Assisted Laser Desorption Ionization) (A)</p> Signup and view all the answers

What does the MS/MS approach in tandem mass spectrometry mainly measure?

<p>Fragmentation spectra (C)</p> Signup and view all the answers

During Protein Identification by Peptide Mass Fingerprinting (PMF), what is the role of endoprotease?

<p>To digest the unknown protein (D)</p> Signup and view all the answers

Which of the following approaches is NOT used for quantitative proteomics?

<p>Protein digestion with basic amino acids (A)</p> Signup and view all the answers

What characteristic does Electrospray Ionization (ESI) provide to ions formed?

<p>Multiply charged ions (D)</p> Signup and view all the answers

What is the purpose of comparing the peak list of peptides from MS analysis?

<p>To match with theoretical peptide peak lists from a database (D)</p> Signup and view all the answers

What is an advantage of isotope labeling in mass spectrometry?

<p>Improves sensitivity and selectivity (B)</p> Signup and view all the answers

What does an increase in salivary pro-inflammatory IL-1β and TNF-α indicate in COVID-19 patients?

<p>Heightened inflammatory response (B)</p> Signup and view all the answers

What type of chromatography is associated with a polar stationary phase and a non-polar solvent?

<p>Normal Phase Chromatography (D)</p> Signup and view all the answers

How is the concentration of a component determined in mass spectrometry-based proteomics?

<p>By assessing the peak area relative to a standard (D)</p> Signup and view all the answers

In a proteomics workflow, which instrument is primarily responsible for the detection phase?

<p>Spectrometer (B)</p> Signup and view all the answers

What is a primary characteristic of High Performance Liquid Chromatography (HPLC)?

<p>It operates under high pressure to enhance separation efficiency. (A)</p> Signup and view all the answers

Which of the following techniques can be used for detection during proteomic analysis?

<p>Fluorometric detection (A)</p> Signup and view all the answers

What is the primary role of the mobile phase in liquid chromatography?

<p>To provide a medium for component separation (B)</p> Signup and view all the answers

What does the peak area in chromatography indicate?

<p>The concentration of a component in the sample (B)</p> Signup and view all the answers

Which pro-inflammatory cytokines were found to be elevated in COVID-19 patients according to the immunoassay results?

<p>IL-1β and TNF-α (C)</p> Signup and view all the answers

What is a disadvantage of using normal phase chromatography?

<p>It is less effective for hydrophilic substances. (B)</p> Signup and view all the answers

Which method is suitable for measuring electrical signals during chromatographic detection?

<p>Conductivity detection (A)</p> Signup and view all the answers

What component is specifically compared to measure the concentration of a target in chromatography?

<p>A reference peak area (C)</p> Signup and view all the answers

What is implied by high levels of IL-6 in COVID-19 patients?

<p>Increased inflammation and tissue damage (A)</p> Signup and view all the answers

What distinguishes reverse phase from normal phase liquid chromatography?

<p>The stationary phase in reverse phase is non-polar. (D)</p> Signup and view all the answers

Flashcards

Qualitative ELISA

A laboratory test that determines if a specific antigen or antibody is present in a sample. It provides a yes/no answer.

Quantitative ELISA

A laboratory test that measures the amount (concentration) of a specific antigen or antibody in a sample.

Titer

The highest dilution of a sample (usually serum) that still gives a positive result in a test.

Multiplex Immunoassay

A technique that allows the simultaneous detection of many different analytes (molecules) in a single sample.

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Color-coded microspheres (beads) in multiplex immunoassay

Beads with different colors and fluorescent properties. Each bead is specific to a particular analyte and can be identified by its color and fluorescence signature.

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What is the proteome?

The complete set of proteins produced by an organism at a given time. It is much more complex than the genome due to alternative splicing, post-translational modifications, and other factors.

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What is proteomics?

The study of proteins, their structures, functions, and interactions. It involves analyzing the proteome to understand biological processes, disease mechanisms, and drug targets.

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What is a proteomics workflow?

A series of steps used to analyze the proteome in detail. It involves sample preparation, protein separation, detection, identification, and functional analysis.

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What is ELISA?

A type of assay used to measure specific proteins in biological samples, such as serum or cell culture supernatant. It is based on the principle of antibody-antigen interactions.

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What are Antibody-based methods in proteomics?

It refers to the use of antibodies to recognize and bind specific target proteins in a sample. These methods are commonly used for protein detection, quantification, and purification.

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What are Protein Separation Techniques?

Methods that separate proteins based on their size, charge, or other physical properties. Examples include gel electrophoresis and chromatography.

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What are Protein Detection Methods?

Methods used to detect and analyze proteins after separation, such as staining or mass spectrometry.

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What is protein identification?

The process of identifying the specific proteins present in a sample. Mass spectrometry and database searching are used to analyze the protein fragments.

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Retention Time in LC

The time taken for a molecule to travel through a chromatography column. It indicates the time it takes for a solute to pass through the column.

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Degree of Separation in LC

The degree to which different components of a mixture are separated in Liquid Chromatography.

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Liquid Chromatography (LC)

A technique used to separate and identify components of a mixture based on their affinity for a stationary phase and a mobile phase. This is commonly used in proteomics to analyze protein mixtures.

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Advantages Of LC

Rapid and efficient separations, Sensitive, selective and non-destructive detectors, Can inject aqueous samples, Low running cost.

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Mobile Phase in Gas Chromatography

A gas (typically Helium or Nitrogen) used as the mobile phase in Gas Chromatography.

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Mass Spectrometry (MS)

An analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in a sample. It is a powerful tool for identifying and quantifying molecules.

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Gas Chromatography (GC)

An analytical technique used to separate and detect small molecular weight compounds in the gas phase.

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Stationary Phase in GC

A thin layer coating the inside of the column in Gas Chromatography. It interacts with the analytes, enabling separation based on their affinities.

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m/z ratio

The ratio of a molecule's mass to its charge, often used in mass spectrometry to identify molecules.

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Mass Spectrometry

A process that separates and identifies molecules based on their mass-to-charge ratio (m/z).

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Proteomics

A type of protein analysis that uses mass spectrometry to identify and quantify proteins in a sample.

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Protein Separation

The process of separating proteins based on their physical and chemical properties.

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Electrospray Ionization (ESI)

A method of ionization used in mass spectrometry where molecules are given a charge by being sprayed into a charged field.

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Matrix Assisted Laser Desorption Ionization (MALDI)

A method of ionization in mass spectrometry where a laser beam is used to vaporize and ionise molecules.

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Ion Trap

A type of mass spectrometer that traps ions in a specific region and allows for multiple measurements of their masses.

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High Performance Liquid Chromatography (HPLC)

A high-performance version of liquid chromatography that uses high pressure to speed up the separation process.

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Tandem Mass Spectrometry (MS/MS)

A technique in mass spectrometry where fragmented molecules are analyzed to determine their amino acid sequence.

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Reverse Phase Chromatography

A type of liquid chromatography that uses a non-polar stationary phase and a polar mobile phase to separate proteins based on their polarity.

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Protein Identification by Peptide Mass Fingerprinting (PMF)

A method for identifying proteins by comparing the masses of the small peptides produced by protease digestion to a database.

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Normal Phase Chromatography

A type of liquid chromatography that uses a polar stationary phase and a non-polar mobile phase to separate proteins based on their polarity.

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Isotope Labeling

A technique used in mass spectrometry to improve sensitivity and accuracy by using isotopes to label molecules.

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Mass Spectrometer

A device that detects and measures the mass-to-charge ratio of ions.

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Peak Area

The measurement of the area under a peak in a chromatogram, which is proportional to the amount of a substance present.

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Standard Reference

A standard solution of a known concentration used to calibrate a measurement system.

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Inflammatory Response

Inflammation caused by an infection.

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Interleukin-1 (IL-1β)

A cytokine involved in the inflammatory response, often elevated in infection.

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Tumor Necrosis Factor-alpha (TNF-α)

A cytokine involved in the inflammatory response, often elevated in infection.

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COVID-19 Inflammatory Profile

Salivary pro-inflammatory cytokines like IL-1β and TNF-α can be increased in individuals with COVID-19, suggesting an inflammatory response.

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Sample Collection

The collection of biological samples such as blood or saliva for analysis.

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Study Notes

Protein Separation and Identification Techniques

  • Techniques used to identify and separate proteins are crucial in various fields, including proteomics.
  • Proteome complexity arises from the large number of proteins in an organism, which vary in size, charge, and structure.
    • The genome encompasses ~20-25,000 genes.
    • The transcriptome represents ~100,000 transcripts.
    • The proteome comprises >1,000,000 proteins.

Proteomics Workflow

  • Proteomics involves a systematic analysis of the entire protein complement (proteome) of a biological sample.
  • The workflow begins with sample preparation, followed by protein extraction and separation.
    • Sample extraction methods include mechanical, chemical, and enzymatic cell disruption.
    • Separation techniques include chromatography, such as centrifugation and electrophoresis.
  • Characterization and analysis of the separated molecules use techniques like NMR, X-ray crystallography, mass spectrometry, and circular dichroism.
  • Identification of the proteins uses various methods, including antibody-based and mass spectrometry techniques.
  • Functional analysis, as well as structural analysis, are subsequent stages.

ELISA (Enzyme-Linked Immunosorbent Assay)

  • ELISA is an immunological assay used for detecting antibodies, antigens, proteins, and glycoproteins in biological samples.
  • Invented by Engvall and Perlman in 1971, ELISA was the first common test for HIV diagnosis.
  • Different ELISA types exist, including direct, indirect, sandwich, and competitive ELISAs.
  • ELISA typically employs 96-well plates for multiple sample analysis.

Multiplex Immunoassay

  • This bead-based immunoassay enables simultaneous detection of up to 100 different analytes.
    • Color-coded microspheres enable distinct spectral signatures.
  • It's used for assessing cytokines and biomarkers in biological samples.

Mass Spectrometry-Based Proteomics

  • Mass spectrometry is a technique used to identify protein constituents in biological samples.
    • Liquid Chromatography (LC) separates protein components.
      • HPLC (High-Performance Liquid Chromatography): a sub-type of LC
      • Gas Chromatography (GC) also used in proteomics
    • Mass spectrometer detects and measures fragments' mass-to-charge ratio (m/z).
      • Various ionization methods exist, including Electron Ionization (EI), Chemical ionization (CI), Fast Atom Bombardment (FAB), Matrix-Assisted Laser Desorption Ionization (MALDI), and Electrospray Ionization (ESI).
    • Tandem mass spectrometry (MS/MS) analyzes fragment spectra for protein identification.
  • Software compares experimental data with theoretical spectra for protein identification.

Protein Identification Strategies

  • Peptide Mass Fingerprinting (PMF) identifies proteins by analyzing the masses of their constituent peptides.
  • Isotope labeling techniques enhance the selectivity and accuracy of protein quantification.
    • Chemical Isotope Labeling (CIL)
    • Multiplex Isotope Labeling methods, such as iTRAQ
  • Various algorithms help assess and compare protein and peptide data. (e.g. MASCOT, Sequest etc.)

Key Findings from the presented information

  • Identification of proteins in a sample requires a combination of protein separation techniques and mass spectrometry analysis.
    • A combination of chromatographic techniques and mass spectrometry (LC-MS/MS, MS/MS) are essential approaches in sample analysis.
  • Different approaches in proteomic studies exist, each with advantages and disadvantages.

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