Proteomics and Mass Spectrometry – Lecture 1 (TAIBMS module)

30 vocabulary flashcards covering key terms, concepts and techniques introduced in Lecture 1 on Proteomics and Mass Spectrometry.

Proteome

The entire set of proteins that is or can be expressed by a cell, tissue or organism at a given time.

Proteomics

The large-scale study and characterization of proteins, including their structures, functions, quantities and interactions.

Human Proteome Atlas

Online resource (proteinatlas.org) that catalogues organ, tissue, cell-cycle and organelle proteomes in humans.

Genome

The complete genetic material (nuclear + mitochondrial) of an organism, including coding and non-coding DNA.

Human Genome Project (2001)

International effort that produced the first draft sequence of the human genome.

2-Dimensional Gel Electrophoresis (2D-GE)

Technique that separates proteins first by isoelectric point (IEF) and then by molecular weight (SDS-PAGE).

Isoelectric Focusing (IEF)

First dimension of 2D-GE where proteins migrate to the pH at which their net charge is zero (pI).

SDS-PAGE

Polyacrylamide gel electrophoresis in the presence of SDS that separates proteins primarily by size.

2-Dimensional Difference Gel Electrophoresis (2D-DIGE)

Variation of 2D-GE that uses fluorescent CyDyes to co-separate and quantitatively compare ≥2 protein samples on a single gel.

CyDyes (Cy2, Cy3, Cy5)

Mass- and charge-matched fluorescent labels used in 2D-DIGE to distinguish different samples.

Mass Spectrometry (MS)

Analytical technique that determines the mass-to-charge ratio (m/z) of ionised molecules to identify and quantify them.

m/z (Mass-to-Charge Ratio)

Value measured in MS; calculated by dividing an ion’s mass (m) by its charge (z).

Soft Ionisation

Gentle ionisation methods (e.g., ESI, MALDI) that allow analysis of large biomolecules without extensive fragmentation; awarded 2002 Nobel Prize in Chemistry.

Electrospray Ionisation (ESI)

MS ion source that generates multiply charged ions from a solution by applying a high voltage to a fine spray.

Matrix-Assisted Laser Desorption/Ionisation (MALDI)

Ion source where a laser pulse ionises analytes embedded in a crystalline matrix; typically yields singly charged ions.

Collision-Induced Dissociation (CID)

Fragmentation method where accelerated ions collide with inert gas, breaking at characteristic peptide bonds for sequencing.

Peptide-Mass Fingerprinting

Identifying proteins by matching experimentally obtained peptide masses (after trypsin digestion) to theoretical masses in databases.

Trypsin

Protease that cleaves peptide bonds at the C-terminal side of lysine (K) and arginine (R), producing MS-friendly peptides.

LC-MS (Liquid Chromatography-Mass Spectrometry)

Coupling of liquid chromatography separation to mass spectrometric detection for complex peptide mixtures.

Ion Source

Part of a mass spectrometer that converts neutral molecules into gas-phase ions under vacuum.

Mass Analyser

Component that separates ions based on m/z (e.g., TOF, Quadrupole, Ion Trap, FT-ICR).

Detector (MS)

Device that registers the number of ions at each m/z value, producing a mass spectrum.

Post-Translational Modification (PTM)

Chemical modification of a protein after translation, such as phosphorylation or glycosylation, contributing to proteome complexity.

Protein Isoform

Different molecular forms of a protein arising from the same gene via alternative splicing or PTMs.

Differential Gene Expression

Variation in gene expression levels between conditions, detectable at the protein level by proteomics.

Proteomics Pipeline

Workflow: sample collection → protein solubilisation → complexity reduction → digestion → peptide clean-up → MS analysis → data processing.

Biomarker Discovery

Use of proteomics to identify protein signatures that differentiate healthy versus diseased states.

Personalised Medicine

Tailoring medical treatment based on individual proteomic (and other ‘omic) profiles.

Proteome Complexity

Increase in molecular diversity from genome to proteome due to splice variants, PTMs, and dynamic regulation.

Peptide Mapping

Generation and MS analysis of peptide fragments from a protein to determine sequence or identity.