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Background: Our aim was to detect differences in protein expression profiles of cerebrospinal fluid (CSF) from pediatric patients with and without brain tumors. Methods: We used surface-enhanced laser desorption/ ionization time-of-flight (SELDI-TOF) mass spectrometry and Q10 ProteinChip arrays to compare protein expression profiles of CSF from 32 pediatric brain tumor patients and 70 pediatric control patients. A protein with high discriminatory power was isolated and identified by subsequent anion-exchange and reversed-phase fractionation, gel electrophoresis, and mass spectrometry. The identity of the protein was confirmed by Western blotting and immunohistochemistry. Results: Of the 247 detected protein peak clusters, 123 were differentially expressed between brain tumor and control patients with a false discovery rate of 1%. Double-loop classification analysis gave a mean prediction accuracy of 88% in discriminating brain tumor patients from control patients. From the 123 clusters, a highly overexpressed protein peak cluster in CSF from brain tumor patients was selected for further analysis and identified as apolipoprotein A-II. Apolipoprotein A-II expression in CSF was correlated with the CSF albumin concentration, suggesting that the overexpres-

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Vascular endothelial growth factor (VEGF) is a key mediator of tumor growth and metastasis. At least 7 isoforms of the protein exist due to differential splicing, but little is known about the biological activities of these different isoforms. We purified VEGF from resected human bronchial carcinoma tissue and normal bronchus by immuno affinity chromatography (IAC) and immuno capture (IC) on a ProteinChip® Array, identifying the isoforms by MS. Both methods proved to be useful for the analysis of protein isoforms, which are present in situ in tumor tissue. Different expression patterns of VEGF were demonstrated in tumor tissue compared to healthy tissue. The possibility to analyse VEGF protein isoforms in situ creates new opportunities to study the regulation of angiogenesis in healthy and malignant tissues.