Table 1.

Quantitative phosphoproteomics in cell lines.

Study (year)	Biological context	Enrichment method	Quantitation	Identified sites	Ref.
Olsen et al. (2006)	HeLa cells EGF-stimulated	TiO2 and SCX	SILAC	6600 phosphorylation sites on 2244 proteins	[5]
Nagaraj et al. (2010)	HeLa	SCX/TiO2		9668 phosphorylation sites	[8]
Rigbolt et al. (2011)	Human stem cells	SCX/TiO2 and others	SILAC	23,522 phosphorylation sites, 6521 proteins	[52]
Beli et al. (2012)	Human osteosarcoma cells (U2OS) treated with etoposide or Ionizing radiation	SCX/TiO2	SILAC	1470 phosphorylation sites (additionally 1796 lysine acetylation sites)	[74]
Mertins et al. (2012)	HeLa cells EGF-stimulated	SCX/IMAC	iTRAQ & mTRAQ	12,129 phosphopeptides on 2699 phosphoproteins (iTRAQ); 4448 phosphopeptides on 1597 phosphoproteins	[77]
Engholm-Keller (2012)	Rat cell line (INS-1)	‘TiSH’: TiO2/sequential elution from IMAC/HILIC		6600 unique phosphopeptides	[35]
Batth et al. (2014)	Mouse 3T3 cells	off-line high-pH chromatography TiO2		30,000 unique phosphopeptide variants	[37]
Bennetzen et al. (2010)	GM00130 cells DNA damage-exposed	ERLIC and TiO2	SILAC	5204 phosphorylation sites	[73]
Bensimon et al. (2010)	G361 human melanoma cell line DNA damage-exposed	TiO2	Label-free	2871 phosphorylation sites on 1099 proteins	[75]
Mertins et al. (2013)	Jurkat cells (human T-cells)	Fe3+-IMAC		20,800 phosphorylation sites	[35]
Sawney et al. (2013)	Yeast	SCX	Label-free	2100 phosphorylation cells, 466 proteins	[107]
Francavilla et al. (2013)	HeLa cells FGF-stimulated	Antiphosphotyrosine beads	SILAC	1212 tyrosine phosphorylated peptides	[71]
KumlerI et al. (2014)	Yeast (rapamycin-treated)	SCX/TiO2	SILAC	8961 phosphorylation sites, 3590 proteins	[136]
de Graaf et al. (2014)	Jurkat cells (human T-cells)	Ti(4+)-IMAC and phosphotyrosine antibody enrichment	Label-free	16,200 phosphorylation sites	[13]
Ruprecht et al. (2015)	Human epidermoid A341 cells	Fe-IMAC in an HPLC format Combined with SCX	Label-free	14,00 unique phosphopeptides	[42]
Giansanti et al. (2015)	Jurkat T-cells	Ti4+-IMAC	Label-free	18,430 unique phosphosites	[31]

Cell studies of phosphoproteomics listing: Biological context of the experiments, Phosphopeptide enrichment method, quantitation method, number of identified sites and reference.

ERLIC: Electrostatic repulsion hydrophilic interaction chromatography; HAMMOC: Hydroxyl acid-modified metal oxide chromatography; iTRAQ: Isobaric tags for relative and absolute quantitation; SCX: Strong cation exchange; TiO₂: Titanium dioxide.