Wilkins 1995 proteome term; O'Farrell 2D-PAGE; Mascot database search; Yates shotgun MS; SILAC; iTRAQ/TMT; XL-MS; DIA-MS; top-down proteomics; spectral counting; protein microarrays; Y2H; AP-MS; CRAPome; phosphoproteomics; Smith-Kelleher…
Proteomics
Wilkins proteome term (1995)
Wilkins et al 1995 Biotechnol Genet Eng Rev; coined 'proteome' (PROTEin complement of the genOME); founded large-scale protein-expression…
O'Farrell 2D-PAGE
O'Farrell 1975 J Biol Chem; two-dimensional PAGE; isoelectric focusing crossed with SDS-PAGE; resolves >1000 cellular proteins; first…
Mascot database search
Perkins-Pappin-Creasy-Cottrell 1999 Electrophoresis; probability-based MS/MS database search; assigns peptides to spectra by matching…
Yates shotgun proteomics
Yates 1996; bottom-up proteomics by trypsin digestion + LC-MS/MS; SEQUEST scoring; transformed protein identification from gel-based to…
SILAC
Ong-Mann 2002 Mol Cell Proteomics; Stable Isotope Labelling with Amino acids in Cell culture; metabolic labelling enables relative…
iTRAQ / TMT isobaric labelling
Thompson-Schafer-Kuhn 2003 TMT; Ross et al 2004 iTRAQ; isobaric tags allow multiplex quantification (up to 18-plex) via reporter-ion…
XL-MS cross-linking mass spec
Rappsilber 2011; Sinz 2003; chemical cross-linking + MS identifies protein-protein interaction interfaces and structural distance…
DIA mass spectrometry
Gillet et al 2012 SWATH-MS; Data-Independent Acquisition; sequential isolation windows fragment all precursors; reproducible quantification…
Top-down proteomics
Kelleher 2004; intact-protein analysis preserves PTM combinations and proteoforms; complements bottom-up; high-resolution FT-MS…
emPAI / spectral counting
Ishihama-Mann 2005; exponentially-Modified Protein Abundance Index; label-free quantification by counting observed-vs-observable peptides…
MacBeath protein microarrays
MacBeath-Schreiber 2000 Science 289:1760; high-density protein-on-glass arrays; screened for kinase-substrate, antibody, small-molecule…
Yeast two-hybrid
Fields-Song 1989 Nature 340:245; reconstitution of GAL4 transcription factor signals protein-protein interaction; founded large-scale…
AP-MS affinity-purification MS
Krogan-Cagney et al 2006; Gavin et al 2002; affinity-purified protein complexes identified by MS; large-scale yeast complexome maps.
CRAPome contaminant repository
Mellacheruvu et al 2013 Nat Methods; database of frequent contaminants in AP-MS; improves specificity scoring and reduces false-positive…
Phosphoproteomics (TiO2 / IMAC)
Pinkse-Mohammed-Mol Cell Proteomics 2004; titanium-dioxide / IMAC enrichment of phosphopeptides; maps kinase-substrate networks at scale.
Smith-Kelleher proteoform
Smith-Kelleher 2013 Nat Methods; 'proteoform' defined as specific molecular form of a protein arising from genetic variation, splicing,…
CPTAC cancer proteome
Clinical Proteomic Tumor Analysis Consortium; integrated genomic + proteomic + phospho-proteomic profiles of common tumours; complements…
Draft human proteome (2014)
Kim et al 2014 Nature 509:575; Wilhelm et al 2014 Nature 509:582; first claimed draft human proteomes; ~17000 protein-coding genes covered;…