Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions. The term proteomics was coined in 1997 in analogy with genomics, the study of the genome. The word proteome is a portmanteau of protein and genome, and was coined by Marc Wilkins in 1994 while he was a PhD student at Macquarie University. Macquarie University also founded the first dedicated proteomics laboratory in 1995 (the Australian Proteome Analysis Facility – APAF).

The proteome is the entire set of proteins that are produced or modified by an organism or system. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes.^[7] Proteomics is an interdisciplinary domain that has benefitted greatly from the genetic information of the Human Genome Project;^[8] it also covers emerging scientific research and the exploration of proteomes from the overall level of intracellular protein composition, structure, and its own unique activity patterns. It is an important component of functional genomics.

While proteomics generally refers to the large-scale experimental analysis of proteins, it is often specifically used for protein purification and mass spectrometry. https://en.wikipedia.org/wiki/Proteomics

Techniques include:

• 2D-SDS PAGE
• Mass spectrometry for peptide and protein analysis.
• HPLC to pre-fractionate complex samples
• Protein Identification by Mass Spectrometry

Protein profiling of complex biological samples, e.g. tissue, cell extracts:

• In-depth proteome analysis using nano LCMSMS Data-dependant acquisition (DDA)
• Off-line basic pH C18 reversed phase chromatography coupled with nan0LC/MSMS analysis
• Multi-dimensional GelCMSMS using 1D  or 2D gel formats

Protein:protein interactions

• Affinity purification of endogenous proteins and their interactiing proteins using Rapid Immunoprecipitation and mass spectrometry of endogenous proteins (RIME);https://www.ncbi.nlm.nih.gov/pubmed/26797456
• Affinity purification of biotinylated proteins using BioID/APEX2/Avitag technologies.
• Affinity purification of tagged fusion proteins using standard immunoprecipitation methods.

Targeted protein identification by nanoLC/MS/MS

• Coomassie and silver stained gel bands of purified proteins
• In solution digestion of purified proteins
• Multiple/parallel reaction monitoring (MRM/PRM)of defined peptides

Identification of protein and peptide modifications

• Phosphoproteomics

Relative quantitation by nanoLC/MS/MS

• Isobaric Labelling with tandem mass tags (TMT)
• SILAC – stable isotope labeling of amino acids in cell culture
• ITRAQ – an isobaric peptide tagging system
• M/PRM: multiple/parallel reaction monitoring