SnapShot: Clinical Proteomics – Key Vocabulary

Vocabulary flashcards covering fundamental terms, techniques, and technologies presented in the lecture on clinical proteomics.

Clinical Proteomics

The large-scale study of proteins in clinical specimens to understand disease states, treatment response, and precision medicine applications.

Liquid Biopsy

Collection of body fluids (e.g., plasma, serum, urine) for molecular analysis without invasive tissue sampling.

Plasma Proteome Dynamic Range

The span of protein abundances in plasma, exceeding ten orders of magnitude and complicating detection of low-abundance proteins.

Extracellular Vesicles (EVs)

Membrane-bound particles released by cells, enriched from blood to access disease-related proteins.

Formalin-Fixed Paraffin-Embedded (FFPE) Tissue

Routine clinical tissue preservation method requiring de-waxing and de-crosslinking before proteomic analysis.

Fresh Frozen (FF) Tissue

Tissue snap-frozen immediately after collection, preserving proteins without chemical cross-linking.

Laser Capture Microdissection (LCM)

Technique that isolates specific cells from tissue sections, enabling spatially resolved proteomics.

Pressure Cycling Technology (PCT)

Semi-automated sample preparation that uses alternating high and low pressure to lyse tissues and extract proteins.

Size-Exclusion Chromatography (SEC)

Chromatographic method that separates proteins or complexes based on molecular size.

Integral Membrane Protein (IMP) Enrichment

Ultracentrifugation under alkaline conditions to isolate low-solubility membrane proteins.

Immunoprecipitation (IP)

Antibody-based isolation of specific proteins or complexes prior to mass spectrometry.

Filter-Aided Sample Preparation (FASP)

Workflow in which proteins are digested on a filter to remove detergents and enhance peptide recovery.

Single-Pot Solid-Phase-Enhanced Sample Preparation (SP3)

Bead-based protocol that binds proteins/peptides to magnetic beads, allowing rapid cleanup and digestion.

In-StageTip (iST) Method

Automated sample prep in miniaturized C18 StageTips, optimized for plasma proteomics.

Tandem Mass Tag (TMT) Labeling

Isobaric chemical tags that enable multiplexed quantification of peptides in data-dependent acquisition.

Nano-flow LC

Liquid chromatography with sub-microliter per minute flow rates, maximizing sensitivity for low-input samples.

Evosep One

High-throughput LC system that embeds peptides in pre-formed gradients for robust clinical proteomics.

Data-Dependent Acquisition (DDA)

MS mode that selects the most intense ions for fragmentation in real time; common in discovery proteomics.

Selected/Multiple Reaction Monitoring (SRM/MRM)

Triple-quadrupole MS technique that quantifies predefined peptides with high sensitivity and specificity.

Parallel Reaction Monitoring (PRM)

High-resolution targeted MS method that records full fragment spectra of selected precursor ions.

Data-Independent Acquisition (DIA)

MS strategy fragmenting all ions within m/z windows, enabling consistent quantification across large cohorts.

Sequential Window Acquisition of All Theoretical Fragment Ions (SWATH)

DIA implementation that systematically cycles through predefined m/z windows.

Ion Mobility Separation

Gas-phase separation based on ion collision cross-section, improving sensitivity and specificity in DIA.

diaPASEF

Method combining ion mobility (PASEF) with DIA to boost speed and depth of proteome coverage.

Scanning SWATH

Ultra-fast DIA technique that continuously scans m/z ranges for high-throughput proteomics.

Absolute QUAntification (AQUA) Peptides

Stable-isotope–labeled synthetic peptides used as internal standards for absolute protein quantification.

Proteoform

Different molecular forms of a protein arising from genetic variation, alternative splicing, or PTMs.

Post-Translational Modification (PTM) Enrichment

Selective isolation of modified peptides (e.g., phosphopeptides) before MS analysis.

Machine Learning in Proteomics

Computational approach for pattern recognition, biomarker discovery, and DIA data interpretation.

Quality Control (QC) in MS

Procedures ensuring instrument performance and data reliability across large clinical cohorts.