Proteomics

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.

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.

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

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.

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.

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

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.

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.

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.

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.