a b s t r a c tIn the frame of protein identification from mouse adipose tissue, two strategies were compared for the offline elution of peptides from a strong cation exchange (SCX) column in two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) analyses. First, the salt gradient (using K + as displacing agent) was evaluated from 25 to 500 mM KCl. Then, a less investigated elution mode using a pH gradient (using citric acid and ammonium hydroxide) was carried out from pH 2.5 to 9.0. Equal amounts of peptide digest derived from mouse adipose tissue were loaded onto the SCX column and fractionated according to the two approaches. A total of 15 fractions were collected in two independent experiments for each SCX elution strategy. Then, each fraction was analyzed on a nanoLC-MS/MS platform equipped with a column-switching unit for desalting and enrichment. No substantial differences in peptide quality characteristics (molecular weight, isoelectric point, or GRAVY [grand average of hydropathicity] index distributions) were observed between the two datasets. The pH gradient approach was found to be superior, with 27.5% more unique peptide identifications and 10% more distinct protein identifications compared with the salt-based elution method. In conclusion, our data imply that the pH gradient SCX fractionation is more desirable for proteomics analysis of entire adipose tissue.Ó 2015 Elsevier Inc. All rights reserved.White adipose tissue (WAT) 3 is a complex metabolic and endocrine organ that secrets a variety of hormones, termed adipokines, into the circulation and thus regulates glucose, lipid, and energy homeostasis in mammalian organisms [1]. Pathological alterations in these various functions are well-established risk factors for metabolic disorders such as obesity, insulin resistance, and type 2 diabetes [2,3]. Investigations aimed at uncovering modifications in WAT protein expression are of important clinical interest in the quest to identify new therapeutic targets or candidate biomarkers for these prevalent pathologies [4,5]. Scientific prominence of adipose tissue proteomics along with an increasing number of adipose tissue proteomics studies per year [6][7][8][9][10][11][12][13][14] was recently observed by Peinado and coworkers [15]. The main hurdles in the isolation and identification of adipose tissue proteins are its high lipid content combined with low protein amount and a high proteome complexity related to significant tissue vascularization and the presence of a multitude of functionally important cell types located in different tissue fractions [4,16,17].Reducing protein sample complexity in two-dimensional liquid chromatography (2D-LC) investigations is a crucial issue. To this effect, various techniques of peptide separation prior to reverse phase liquid chromatography (RPLC) hyphenated to mass spectrometry (MS) detection are employed: electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) [18,19], hydrophilic interaction chromatography (HILIC) [20], ion exch...