Proteomics

Proteomics is the large-scale study of the full set of proteins present in a cell, tissue, or organism at a given time, including their identity, abundance, and chemical modifications, rather than studying one protein in isolation.

Mass spectrometry is the dominant technology: proteins are broken into fragments whose measured masses are matched against reference databases to identify and quantify them, producing datasets that, like genomic data, require substantial computational processing before results are interpretable. This differs from genomic analysis built on sequence alignment, which studies the relatively static DNA sequence, proteomics captures a more dynamic picture, since which proteins are present and how abundant they are changes with cell state, time, and condition, much as expression measured by Single-cell RNA sequencing does at the RNA level.

Because proteins, not genes directly, carry out most cellular function, proteomic changes often track disease or drug response more directly than genomic changes alone, making the field central to biomarker discovery and drug development, and it depends on high-performance computing to process the resulting datasets. Pitfalls include low-abundance proteins that are easily missed, and matching spectra against a reference database can produce confident-looking but incorrect identifications without careful statistical control of the false discovery rate.