Proteomics of Prostate Cancer Figure 1. Outline of the strategy employed in this study (see text for details). Androgen-stimulated LNCaP cells were profiled using both quantitative iTRAQ MALDI- TOF/TOF and semi-quantitative MudPIT ESI- LTQ proteomics platforms. Data from each of these platforms were normalized independently and combined to generate a list of androgen-regulated proteins. This list was interrogated for biological associations using Molecular Concepts Mapping (MCM). The concept describing aminoacyl tRNA synthetases was selected for further examination; selected proteins were validated using immunoblot and immunofluorescence staining. Transcriptomic profiling and chromatin immunoprecipitation showed that androgen drives expression of aminoacyl-tRNA synthases at the transcript level. This was further confirmed using cancer tissue gene expression data and immunoblot analysis on prostate tissue samples, which demonstrated the existence of the elevated aminoacyl-tRNA synthase niche during prostate cancer progression. doi:10.1371/journal.pone.0007075.g001 ribonucleoprotein L isoform a) was common between iTRAQ and MudPIT platforms (Figure 2E). Our list of up-regulated proteins included five proteins that have been shown previously to be elevated by androgen action: ACSL3 (iTRAQ ratio 2.76), FKBP51 (iTRAQ ratio 1.91; MudPIT spectral counts 17:0), FASN (iTRAQ ratio 1.85; MudPIT spectral counts 417:45), NDRG1 (iTRAQ ratio 1.76; MudPIT spectral counts 5:0), and KLK3 (also known as PSA, Prostate Specific PLoS ONE | www.plosone.org 3 September 2009 | Volume 4 | Issue 9 | e7075