Proteins and Proteomics

A comprehensive set of flashcards covering key concepts of mass spectrometry and proteomics for exam review.

What is mass spectrometry?

It's a method to determine the mass-to-charge ratio (m/z) of ions in the gas phase.

What are the two main types of ions formed in mass spectrometry?

Positive ions (M+H)+ and negative ions (M-H)-.

What does mass spectrometry measure?

It measures the mass-to-charge ratio (m/z) of ions.

What is an intrinsic property of matter related to mass spectrometry?

Mass is an intrinsic property of matter.

What type of applications does mass spectrometry have?

It has a wide variety, including protein identification, peptide sequencing, and determining mutations.

What is a major application of mass spectrometry in proteomics?

Protein identification.

What is the function of the ion source in a mass spectrometer?

It creates ions in the gas phase from the sample.

What process involves creating charged ions from molecules?

Ionization.

What does m/z analysis help to achieve in mass spectrometry?

It allows the separation of ions based on their mass-to-charge ratio.

What are isotopes?

Atoms of the same element with different numbers of neutrons.

What is the significance of the base peak in a mass spectrum?

It represents the most abundant ion present.

What is meant by the term resolution in mass spectrometry?

Resolution refers to the instrument's ability to distinguish between different m/z peaks.

How can isotopic patterns be used in mass spectrometry?

Isotopic patterns help to identify the elemental composition of molecules.

What is the role of the detector in a mass spectrometer?

It detects the ions and generates a mass spectrum from the signals.

What does the term 'collisional activation' refer to in ion fragmentation?

It refers to the process where ions collide with gas molecules, causing fragmentation.

What is peptide mass fingerprinting (PMF)?

A technique using mass spectrometry to identify proteins by analyzing peptide masses.

What is one challenge of analyzing protein mixtures with mass spectrometry?

Differentiating between peptides with the same mass.

How does the electrospray ionization (ESI) method work?

It creates a spray of charged droplets from a sample solution for mass spectrometry analysis.

What is Matrix-Assisted Laser Desorption/Ionization (MALDI)?

A method that uses a laser to ionize samples mixed with a matrix.

Why is sample purity important in ESI?

Impurities can interfere with ionization and affect mass spectrometry results.

What is the advantage of using tandem mass spectrometry (MS/MS)?

It allows for detailed sequencing of peptides by fragmenting ions.

What is the difference between 'monoisotopic mass' and 'average mass'?

Monoisotopic mass refers to the mass of the most abundant isotope, while average mass is weighted by all isotopes.

What does the term 'charge deconvolution' in ESI mean?

It is the process of determining the charge state of ions from multiple peaks.

What can the isotopic pattern in a mass spectrum reveal?

It can provide information about the molecular formula of a compound.

What factors influence the resolution of mass spectrometry?

Instrument design, ionization method, and the properties of the sample.

What is the role of the mass analyzer in mass spectrometry?

To separate ions based on their m/z before detection.

What is a common approach for protein separation before mass spectrometry?

Two-dimensional gel electrophoresis.

How does liquid chromatography (LC) improve mass spectrometry results?

It separates proteins/peptides before ionization and analysis.

What is the significance of angular momentum in the Orbitrap analyzer?

It allows the measurement of ion frequencies and high-resolution analysis.

In peptide sequencing, what are b-ions and y-ions?

b-ions are N-terminal fragments; y-ions are C-terminal fragments.

What is the purpose of using a gas during fragmentation in tandem MS?

To collide with ions and induce fragmentation.

How does post-translational modification (PTM) affect mass spectrometry results?

PTMs can change the mass of peptides, affecting their identification.

What does 'false discovery rate' (FDR) refer to in mass spectrometry?

The expected proportion of false positives among identified proteins.

What is a common method for confirmation of identified proteins?

Database searching against theoretical peptide spectra.

What kind of information can mass spectrometry provide about protein structures?

It can offer insights into molecular weight and structural changes.

What are the primary purposes of structural proteomics?

Determining protein structures and interactions.

What type of study is 'shotgun proteomics'?

A strategy to identify many proteins in a single sample run.

What baseline assumptions does peptide mass fingerprinting rely on?

That each protein can be represented by the unique masses of identifiable peptides.

What is the main advantage of using liquid chromatography prior to mass spectrometry?

Improved separation of complex mixtures, enhancing detection accuracy.

What is critical to ensure prior to mass analysis in proteomics?

Sample purification is necessary to prevent contamination.

In mass spectrometry, what does 'deconvolution' achieve?

It determines the actual molecular mass from multiple overlapping peaks.

What does 'average mass' represent in mass spectrometry?

The weighted average mass considering all isotopes of an element.

How is protein identification typically validated in mass spectrometry?

Through matching experimental data to protein sequence databases.

Why are stable isotopes important in mass spectrometry?

They help in determining the isotopic pattern and molecular composition.

What characterizes the mass spectrum of a peptide?

It shows peaks corresponding to the m/z ratios of various peptide fragments.

In protein analysis, what does the term 'short gradients' refer to?

The use of short separation times to improve resolution in LC.

What does a high charge state indicate in ESI?

That the analyte has gained multiple protons during ionization.

How does MALDI improve sensitivity in mass spectrometry?

By allowing low concentrations of analytes to be analyzed without fragmentation.

Why is the mass defect important in mass measurements?

It helps in accurate mass determination by accounting for isotopic variations.

In protein characterizations, what does 'cross-linking' help establish?

Proximity relationships between amino acids in a protein structure.

What does HDX-MS reveal about protein structure?

Dynamics and solvent accessibility of amide hydrogens.

How does pH influence hydrogen-deuterium exchange rates?

Lower pH slows the exchange process for amide protons.

What is the significance of analyzing timing in hydrogen-deuterium exchange experiments?

Timing impacts the assessment of solvent accessibility in proteins.

What is one primary challenge in shotgun proteomics?

Identifying overlapping peptides from complex samples.

What technique is primarily used to cleave proteins for mass spectrometry analysis?

Enzymatic digestion, commonly with trypsin.

What percentage of sequence coverage typically indicates a confident protein identification?

Higher coverage leads to improved confidence in the identification.

How does using multiple charge states in ESI enhance analysis?

It allows larger proteins to be analyzed effectively.

What does intensity distribution in a spectrum indicate?

The relative abundance of different ions within the mixture.

What is the role of data systems in mass spectrometry?

To control, store, and analyze the data collected from the detector.

What can analyze different aspects of the same sample in tandem MS?

Combining multiple analyzers, like a quadrupole and an Orbitrap.

What is the overall goal of proteomics?

To identify and quantify all proteins within a complex sample.

In mass spectrometry, what does 'sample ionization' refer to?

The conversion of neutral samples into charged ions for analysis.

What is unique about cross-linking mass spectrometry (XL-MS)?

It measures distances between amino acids linked by cross-linkers.

What enables mass spectrometry to provide insights into protein dynamics?

Techniques like HDX that measure solvent exchange rates.

What method of chromatography is favored for peptide separation?

Liquid chromatography is the most common method.

What can contribute to spectral redundancy?

Repeated observations of the same peptide in mass spectra.