Proteomics Cheat Sheet

The core ideas of Proteomics distilled into a single, scannable reference — perfect for review or quick lookup.

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Quick Reference

Mass Spectrometry (MS)

An analytical technique that measures the mass-to-charge ratio of ions to identify and quantify molecules. In proteomics, tandem mass spectrometry (MS/MS) fragments peptides and matches their spectra to protein databases for identification.

Two-Dimensional Gel Electrophoresis (2-DE)

A protein separation technique that resolves proteins in two steps: first by isoelectric point (charge) and then by molecular weight, producing a map of spots where each spot represents one or more protein species.

Post-Translational Modifications (PTMs)

Chemical modifications that occur on proteins after translation, such as phosphorylation, glycosylation, acetylation, and ubiquitination. PTMs regulate protein activity, localization, interactions, and degradation.

Protein-Protein Interactions (PPIs)

Physical contacts between two or more proteins that occur through molecular recognition. Mapping PPI networks reveals how proteins collaborate in signaling pathways, complexes, and cellular processes.

Shotgun Proteomics

A bottom-up approach in which a complex protein mixture is enzymatically digested into peptides, separated by liquid chromatography, and analyzed by tandem mass spectrometry without prior protein-level separation.

Quantitative Proteomics

Methods for measuring relative or absolute protein abundance across samples. Approaches include label-free quantification, metabolic labeling (SILAC), and chemical labeling (TMT, iTRAQ).

Proteome

The entire complement of proteins expressed by a genome, cell, tissue, or organism at a specific time and under specific conditions. Unlike the genome, the proteome is dynamic and context-dependent.

Biomarker Discovery

The process of identifying measurable biological indicators (proteins, peptides, or PTMs) that correlate with a disease state, prognosis, or treatment response, typically using comparative proteomic analysis.

Data-Independent Acquisition (DIA)

A mass spectrometry acquisition strategy that systematically fragments all ions within predefined mass windows, generating comprehensive and reproducible datasets that can be mined computationally for protein identification and quantification.

Structural Proteomics

The large-scale determination of three-dimensional protein structures using techniques such as X-ray crystallography, cryo-electron microscopy, and nuclear magnetic resonance, often aided by computational prediction tools like AlphaFold.

Key Terms at a Glance

Proteome:The complete set of proteins expressed by a cell, tissue, or organism under defined conditions.

Mass Spectrometry:An analytical technique that measures the mass-to-charge ratio of ions for molecular identification and quantification.

Tandem Mass Spectrometry (MS/MS):A technique involving two stages of mass analysis: precursor ion selection and fragmentation followed by fragment ion detection.

Liquid Chromatography (LC):A separation technique that partitions analytes between a liquid mobile phase and a stationary phase, used to reduce sample complexity before MS.

Two-Dimensional Gel Electrophoresis:A protein separation method using isoelectric focusing and SDS-PAGE to resolve proteins by charge and molecular weight.

Post-Translational Modification (PTM):A covalent chemical modification to a protein after its synthesis, regulating its activity, localization, or interactions.

Phosphorylation:The addition of a phosphate group to serine, threonine, or tyrosine residues, a key regulatory PTM in cell signaling.

Glycosylation:The attachment of sugar moieties to proteins, affecting folding, stability, and cell-cell recognition.

Ubiquitination:The attachment of ubiquitin to a protein, often signaling it for proteasomal degradation.

SILAC:Stable Isotope Labeling by Amino acids in Cell culture, a metabolic labeling method for quantitative proteomics.

TMT:Tandem Mass Tags, isobaric chemical labels enabling multiplexed quantitative comparison of protein abundance.

iTRAQ:Isobaric Tags for Relative and Absolute Quantification, a chemical labeling method for multiplexed proteomics.

Label-Free Quantification:A quantitative proteomics strategy estimating protein abundance from peptide ion intensities or spectral counts without isotopic labels.

Data-Independent Acquisition (DIA):An MS strategy that fragments all precursor ions in systematic m/z windows for comprehensive and reproducible analysis.

Electrospray Ionization (ESI):A soft ionization method producing multiply charged ions from solution-phase analytes, standard for LC-MS proteomics.

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