Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, ϳ400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.

Shared senior authorshipWhat's known on the subject? and What does the study add?• The current basis for diagnosis and prognosis in urinary bladder cancer is based on the pathologists' assessment of a biopsy of the tumour. Urinary biomarkers are preferable as they can be non-invasively sampled. Urinary cytology is the only test with widespread use but is hampered by poor reproducibility and low sensitivity.• By studying the protein expression in bladder tumour tissue samples of proteins previously found in elevated levels in the urine of patients with bladder cancer, we have been able to show that these proteins originate from the tumour. The immunoreactivity of three of the investigated proteins increased with higher stage. Also a serine peptidase inhibitor was found to be predictive of progression from non-muscle-invasive to muscle-invasive tumours. Objectives• To analyse the expression of five bladder cancerassociated urinary proteins and investigate if expression is related to the malignant phenotype of the tumour.• To explore the possible prognostic value of these proteins. Patients and Methods Results• Increased expressions of APOE, FGB and POLR1E were correlated with increased tumour stage (P < 0.001).• Expression of SERPINA1 in Ta and T1 tumours was found to increase the risk of tumour progression (hazard ratio 2.57, 95% confidence interval 1.13-5.87; P = 0.025) Conclusions• All proteins previously detected in urine from patients with bladder cancer were also expressed in bladder cancer tissue. • The expression of APOE, FGB and POLR1E increased with stage and they are potential diagnostic markers. • SERPINA1 was identified as a prognostic marker candidate.