Table 1.

Research examples of diabetes and obesity studies using proteomic tools

Tool	Sample	Resulting data	Ref.
2DE silver MALDI-TOF	Plasma proteins/blood-sera in ob/ob mice that are obese because of the lack of leptin	EPS is a potent gene expression regulator (in ob/ob mice) in obesity, insulin resistance and DM. Ferritin and adiponectin as important factors for future DM2.	33
		Expression level of Apo A-I, IV, C-III, E, retinol-binding protein 4 and transferrin were shown to be altered and their levels are normalized after EPS treatment.
		Resistin is up-regulated while adiponectin is down-regulated in diabetes and obesity.
2DE-DIGE MALDI-TOF	Adipose tissue	9 higher expressed proteins in the adipocytes from old compared to young obese patients:	92
		Prohibitin 1
		Protein disulphide isomerase A3
		Beta actin
		Profilin
		Aldo-ketoreductase 1 C2
		Alpha crystallin B
		Anexins A1, A5, A6
		4 lower expressed proteins in the adipocytes from old compared to young obese patients:
		Keratin type 2 cytoskeletal 1
		Keratin type 2 cytoskeletal 10
		Haemoglobins A, B
		Signal transducer and activator of transcription 3 as the central molecule in the connectivity map and the apoptosis pathway
iTRAQ LC-MS/MS	Heart tissue	29 proteins up-regulated from a total of 1.627, while 84 were down-regulated in the db/db mice compared with the control group	93
		Calnexin was found to be decreased whereas integrin-linked protein kinase was decreased in the phlorizin treated DM group compared with the DM group
SDS-PAGE LC-MS/MS/MS LTQ-FT ELISA	Subcellular fractionation of the mouse preadipocyte cell line 3T3-L1 with and without insulin treatment into cytosol, membrane, mitochondria and nuclear fractions and nuclear fractions	3.287 identified proteins that form part of the adipocyte proteome	94,95
	Genetically modified animal models (bGH, GHA and GHR−/− mice and tissue-samples	Useful information to unravel the complexity of the adipocyte in obesity
		Addressed that adiponectin is generally negatively associated with GH activity, regardless of age
		Useful information about the associations of total and HMW adiponectin with insulin sensitivity and longevity
		Circulating adiponectin levels correlated strongly with inguinal fat mass, implying the effects of GH on adiponectin are depot-specific
Phosphoproteomics SILAC anti-pY immunoprecipitation	Brown adipocytes	From the 40 insulin effectors identified, 7 (SDR, PKC binding protein, LRP-6 and PISP/PDZK11, a potential calcium ATPases binding protein	96
2DE-gels stained by Sypro-Ruby	Platelet-free plasma from the patients	53 differentially spot-proteins from which 51% were shown to be down-regulated comparing Vit D deficiency	97
		The HMW form of adiponectin is down-regulated in obese paediatric patients with Vit D deficiency
		Thrombospondin 1 (TSP1) is up-regulated while histone deacetylase 4 (HDAC4) is down-regulated
SCX MS/MS	Peripheral blood mononuclear cells	TSP1 and HDAC4 recover their normal expression level due to physical exercises	98
2DE-gels LC-MS/MS MALDI-TOF MS	Liver sample	A diet rich in n-3PUFA decreases the expression of regucalcin, aldehyde dehydrogenase	99
		A diet rich in n-3 PUFA increases
		the expression of a POLI protein-A-1, S-adenosylmethionine synthase, fructose 1,6 biphosphatase, ketohexokinase, malate dehydrogenase, GTP-specific succinyl CoAsynthase, Ornithine aminotransferase, protein disulfide isomerase A3
2DE-gels MALDI-TOF MS and MS/MS	Human subcutaneous (SQ) and white adipose tissue (WAT)	The levels of several proteins in human SQ-WAT are not homogeneous between different WAT depots	100
		Twenty-one proteins showed differential intensities among the six defined anatomical locations, and 14 between the superficial and the deep layer (such as vimentin, heat-shock proteins, superoxide-dismutase, fatty acid-binding protein, alpha-enolase, ATP-synthase among others)
2DE-DIGE MALDI-TOF MS and MS/MS	Visceral adipose tissue (VAT) from pre-obese diabetic patients	The presence of diabetes influences the VAT abundance of several proteins	83
		Diabetic patients showed increased VAT abundance of glutathione S-transferase Mu 2, peroxiredoxin-2, antithrombin-III, apolipoprotein A-IV, Ig κ chain C region, mitochondrial aldehyde dehydrogenase and actin, and decreased abundance of annexin-A1, retinaldehyde dehydrogenase-1 and vinculin, compared with their non-diabetic counterparts.
Label-free quantitative proteomics	Salivary samples from patients with diabetes	This study demonstrates that differences exist between salivary proteomic profiles in patients with diabetes based on the A1C levels	84
2DE MALDI-TOF MS and MS/MS	Serum samples from obese children	This research study establishes the bases of the utility of proteomics to assess clinical improvements in obesity.	85
		Down-regulated proteins in obese patients: transthyretin apolipoprotein-A1, apo-J/clusterin and vitamin D binding protein.
		ApoA1 was further down-regulated under the presence of up-regulation insulin resistance, whereas weight reduction induced its up-regulation.
		Apolipoprotein-A1 and haptoglobin were validated via ELISA as true potential candidate biomarkers

Representative assays detailing in each column –the goals, technologies, type of sample to be analysed and the resulting data– are placed schematically in this table. 2DE-electrophoresis is one the most common tools used in diabetes and obesity research studies when using proteomics. Nevertheless, currently, more scientific articles are appearing and showing the advantages when applying HPLC or nano-HPLC coupled directly to mass spectrometry (LC-MS) to avoid losing low expressed proteins or putative biomarkers. Biomarkers, adipocyte and insulin proteomes have been the most common goals followed by scientists to unravel diabetes and obesity pathologies. All of them –and many others– allowed us to advance and establish the right platforms and current technology-innovations will permit improve diagnoses and refine therapies via identifying new biomarkers by proteomics.