Proteomics, MS and Biomedical Applications – Vocabulary

Vocabulary flashcards covering essential terms and concepts from the lecture on proteomics, mass spectrometry, quantitative strategies and biomedical applications.

Proteomics

The large-scale study of proteins, including their identities, quantities and modifications.

Proteome

The entire set of proteins produced or modified by an organism, tissue or cell system.

Mass Spectrometry (MS)

Analytical technique that measures ions’ mass-to-charge ratios to identify and quantify molecules.

LC-MS/MS

Coupled liquid chromatography and tandem mass spectrometry workflow for peptide separation and sequencing.

Liquid Chromatography (LC)

Technique that separates peptides in solution before ionisation and MS analysis.

High-Performance Liquid Chromatography (HPLC)

Pressure-driven LC variant that provides high resolution peptide separations.

Electrospray Ionisation (ESI)

Soft ionisation method producing multiply charged peptide ions directly from liquid effluent.

MALDI

Matrix-Assisted Laser Desorption Ionisation; lower-throughput, plate-based ionisation for MS.

Mass-to-charge ratio (m/z)

The parameter measured by MS; mass of an ion divided by its charge state.

Peptide Sequencing

Deriving amino-acid order from fragmentation spectra in MS/MS.

abc / xyz ion series

Nomenclature describing N-terminal (a,b,c) and C-terminal (x,y,z) peptide fragments.

Trypsin

Protease that cleaves on the C-terminal side of lysine and arginine residues during digestion.

Enzymatic Digestion

Proteolysis step turning proteins into peptides suitable for MS analysis.

MS1

First MS stage that records survey scan of intact peptide precursor ions.

MS2 (MS/MS)

Second MS stage that fragments selected precursors and records their product-ion spectra.

Peptide Spectrum Matching

Probability-based assignment of MS/MS spectra to peptide sequences in a database.

Quantitative Proteomics

MS strategies aimed at measuring differences (relative or absolute) in protein abundance.

Absolute Quantification

Determining actual concentration of a protein via calibrated standards.

Relative Quantification

Assessing fold-changes between conditions without knowing absolute concentrations.

Stable Isotope Labelling

Incorporation of heavy isotopes (e.g., 13C, 15N) to create mass-distinguishable peptide pairs.

SILAC

Stable-Isotope Labelling with Amino acids in Cell Culture; metabolic incorporation prior to lysis.

Tandem Mass Tag (TMT)

Isobaric chemical tags that allow multiplexed peptide labelling and MS2-based quantification.

iTRAQ

Isobaric tagging method similar to TMT for post-digestion peptide labelling.

Label-free Quantification (LFQ)

Quantitation based on ion intensities or spectral counts across separate MS runs, without isotopes.

Spectral Counting

Label-free metric that infers protein abundance from the number of identified MS/MS spectra.

Targeted Proteomics

Pre-programmed MS acquisition focusing on selected peptides for high-accuracy quantification.

Discovery-based Proteomics

Unbiased approach aiming to identify as many proteins as possible in a sample.

Selected Reaction Monitoring (SRM)

Targeted method where specific precursor/product ion pairs are measured on a triple quadrupole.

Multiple Reaction Monitoring (MRM)

SRM variant monitoring many transitions in one run.

Triple Quadrupole (QQQ)

MS instrument with three quadrupoles used for SRM/MRM experiments.

Data-Independent Acquisition (DIA)

Acquisition mode fragmenting all ions in wide m/z windows, enabling comprehensive quantification.

SWATH-MS

Sequential Window Acquisition of all Theoretical Mass Spectra; a DIA strategy generating digital maps.

Data-Dependent Acquisition (DDA)

Discovery mode where the most intense precursors in MS1 are automatically selected for MS2.

Volcano Plot

Statistical graph plotting fold-change versus significance to highlight differential proteins.

Principal Component Analysis (PCA)

Dimensionality-reduction technique used to visualise sample variance in proteomics datasets.

Hierarchical Clustering

Method that groups proteins or samples based on similarity in abundance patterns.

Protein-Protein Interaction (PPI) Network

Graph representation of proteins (nodes) and their interactions (edges) derived from data.

Extracellular Matrix (ECM)

Network of proteins and polysaccharides surrounding cells and studied via MS for composition.

Integrins

Transmembrane adhesion receptors linking cells to the ECM and mediating bidirectional signalling.

Adhesome

Collection of proteins associated with integrin-based adhesion complexes.

Phosphoproteomics

Proteomic subset focused on identifying and quantifying phosphorylated peptides and proteins.

BioID

Proximity-dependent biotinylation technique using BirA* to label proteins near a bait in vivo.

Proximity-dependent Labelling

Spatial proteomics methods (e.g., BioID, APEX) marking proteins within nanometres of a target.

Rapid Evaporative Ionisation MS (REIMS)

Ambient MS technique detecting vapourised tissue aerosols, utilised by the iKnife.

iKnife

Electrosurgical knife coupled to REIMS providing intraoperative molecular fingerprints of tissue.

MS Imaging

Technique creating spatial maps of molecule distributions directly from tissue sections.