Lecture 4 FC Proteomics Lecture Notes

Flashcards providing vocabulary terms and definitions related to proteomics, mass spectrometry, and their applications, based on the provided lecture notes.

MCOM Proteomics Core Facility

Supports researchers with state-of-the-art mass spectrometry instrumentation and bioinformatic tools for routine and customized proteomics analysis, offering training, experimental design, and sample preparation.

Proteomics

The study of the proteome, assessing the activities, modifications, and interactions of proteins within a cell, tissue, or organism to determine their function.

Proteome

The complete set of proteins expressed by a cell, tissue, or organism at a specific time, which is fluid and changes based on conditions.

Genome

The complete set of genetic material in an organism; it is static.

Proteome (contrast with genome)

The dynamic and fluid population of proteins present at a given time, which can differ even with the same genome.

Amino Acids

The basic building blocks of peptides and proteins, each containing an amino group, a carboxyl group, and a unique side chain (R group).

Peptides

Chains of amino acids linked by peptide bonds, which are smaller than proteins.

Protein

A large complex molecule made up of one or more long chains of amino acids (peptides) folded into a specific three-dimensional structure, essential for various bodily functions.

Interdisciplinary Nature of Proteomics

Combines fields such as Analytical Chemistry, Bioinformatics, Medicine & Research, Mass Spectrometry, Protein Chemistry, and Cell and Molecular Biology to study proteins.

Basic Proteomics Protocol

Involves sample preparation (lysis, digestion), peptide separation (RP-UPLC), mass spectrometry analysis (Full MS, MS/MS), database searching for protein identification, and bioinformatic analysis for quantification and interpretation.

HPLC (High Pressure Liquid Chromatography)

A separation technique used in proteomics, employing a column with a stationary phase (e.g., RP-UPLC) to separate peptides based on their properties before mass spectrometry.

Mass Spectrometry (MS)

An analytical technique that measures the mass-to-charge ratio (m/z) of ions, consisting of an ion source, a mass filter (analyzer), and a detector, used to identify and quantify molecules.

Ion Source (Mass Spectrometry)

A component of a mass spectrometer that converts sample molecules into gas-phase ions, examples include Electrospray Ionization (ESI) and MALDI.

Mass Analyzer (Mass Spectrometry)

A component of a mass spectrometer that separates ions based on their mass-to-charge (m/z) ratio, examples include TOF, Quadrupole, and Ion Trap.

Detector (Mass Spectrometry)

A component of a mass spectrometer that measures the abundance of separated ions, such as a multichannel plate or cyclotron.

Principle of Mass Spectrometry

Ions with different charges and masses move distinctly in magnetic or electrical fields, allowing for their separation and measurement by a mass analyzer. Selected ions can then be fragmented and measured again (MS/MS).

m/z ratio

The mass-to-charge ratio of an ion, measured in mass spectrometry, which provides information about the molecular weight.

Ion Intensity (Mass Spectrometry)

The relative abundance of a particular ion detected in mass spectrometry, used to quantify components between samples.

Monoisotopic Mass

The exact mass of a molecule using the masses of the most abundant isotope for each element, which is typically measured in high-resolution mass spectrometry.

MS/MS (Peptide Fragmentation)

Tandem mass spectrometry where selected ions are fragmented (e.g., peptides) into smaller ions, and their m/z ratios are measured to determine amino acid sequence or structural information.

Peptide Sequence Determination (Mass Spec)

Enabled by MS/MS data, as different peptides with the same intact mass can be distinguished by their unique fragmentation patterns.

Global Proteome Profiling

A comprehensive approach in proteomics to discover proteins, profile protein expression changes (e.g., in disease or drug treatment), identify biomarkers, and predict regulatory and functional outcomes through bioinformatic analysis.

Biomarker

A quantifiable indicator of a biological state or condition, often identified through global proteome profiling, useful for diagnosing diseases or monitoring drug treatment effects.

Relative Quantification Strategies (Proteomics)

Methods used to compare protein abundances between different samples, including stable isotope labeling (SILAC, iTRAQ, TMT) and label-free approaches.

SILAC (Stable Isotope Labeling by Amino Acids in Cell Culture)

A relative quantification strategy in proteomics where cells are grown in media containing "heavy" or "light" isotopically labeled amino acids to distinguish proteins from different samples.

iTRAQ (Isobaric Tag for Relative and Absolute Quantitation)

A relative quantification strategy using isobaric tags that label peptides, allowing for simultaneous identification and quantification of proteins from multiple samples in a single mass spectrometry run.

TMT (Tandem Mass Tagging)

A relative quantification strategy similar to iTRAQ, employing isobaric labels that allow for multiplexed peptide quantification and identification in mass spectrometry.

Immunoprecipitation Analysis (Proteomics)

A technique used to isolate a specific protein or protein complex using antibodies, often followed by mass spectrometry to identify the protein of interest, its interacting partners, or co-purified subunits.

Post-Translational Modifications (PTMs)

Chemical modifications of a protein after its translation, such as phosphorylation, ubiquitination, and acetylation, which can alter its function, localization, or interaction with other molecules.

Ingenuity Pathway Analysis (IPA)

A bioinformatics tool used to interpret large-scale proteomic data by identifying statistically significant biological functions, canonical pathways, upstream regulators, and networks affected by observed protein changes.

Proteomics in Personalized Cancer Care

Applied to screening, biomarker discovery, understanding drug mechanisms, preclinical modeling, and patient monitoring with quantitative mass spectrometry to tailor treatments.

Proteomics in Coral Bleaching Research

Used to study protein changes in corals during bleaching, identifying differences in heat shock proteins, apoptosis, biomineralization, and UV responses, as shown by Ricaurte et al. (2016).

"Fossil-omics"

The application of proteomics to study ancient protein samples, such as bones from permafrost, involving demineralization, digestion, and mass spectrometry to identify proteins while accounting for amino acid degradation and substitution.