Background: We examined, for the first time proteins expressions and abundancies within paired human subcutaneous (SAT) and visceral adipose tissues (VAT), using equal amounts of fully digested proteins.

Methods: Fully digested protein preparations from white adipose tissues biopsies of an obese male patient were analyzed both directly and after prior fractionation using LC-MS/MS. Data were processed to yield identified proteins and protein abundances. Proteins were annotated to the three Gene Ontology (GO) domains: Cellular Components (CC), Biological Processes (BP) and Molecular Functions (MF).

Results: Without prior fractionation, 519 proteins were identified in SAT and 567 in VAT. The tissues had 458 proteins in common, accounting for 90% and 83% of identified proteins in SAT and VAT, respectively. With prior fractionation, 1307 proteins were identified in SAT and 1710 in VAT. The tissues had 1248 proteins in common, accounting for 95% and 73% of identified proteins in SAT and VAT, respectively. Semi-quantitative proteins abundances were compared for proteins occurring in common, unveiling large differences between the two tissues. Substantial differences were found in GO annotated proteins abundances, unique to either SAT or VAT, concerning extracellular, nucleus, cytoplasm, and membrane (CC), metabolic process and cellular component movement (BP), metal ion binding, nucleotide binding, RNA binding, protein binding and DNA binding (MF).

Conclusion: The proteomes of paired human adipose tissues reflect both common and unique proteins and semi-quantitative proteins abundances. Our holistic analysis accounts as an alternative approach to look for biological differences between SAT and VAT in white adipose tissues.