Data-independent proteome analysis of ARPE-19 cells

We have performed a proteomics analysis of a human retinal pigment epithelial cell line (ARPE-19), which represents a widely used model for in vitro studies of cellular and molecular mechanisms related to human RPE cells (Dunn et al., 1996; Weigel et al., 2002) [1], [2]. Whole cell protein extracts were separated in four gel fractions via short (10 min) SDS-PAGE runs. Following fractionation and trypsin digestion, the resulting peptides were separated on a nano UPLC LC system and analyzed on-line with a QTof-IMS instrument: a tandem mass spectrometer with ion mobility separation (Synapt G2-Si). Data were acquired in data-independent mode (UDMS(E)), which allows for absolute and/or relative post-acquisition protein quantification (Silva et al., 2006) [3]. The proteome profile data obtained from this study can be used as a protein reference database with qualitative and quantitative protein information related to ARPE-19 cells under normal growth conditions.