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Molecular & Cellular Proteomics 4:637-650, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

A Proteomic Analysis of Human Hemodialysis Fluid^*,S

Henrik Molina^,, Jakob Bunkenborg^,,¶, G. Hanumanthu Reddy^||, Babylakshmi Muthusamy^||, Paul J. Scheel^** and Akhilesh Pandey^,

From the McKusick-Nathans Institute for Genetic Medicine and Department of Biological Chemistry and Oncology and the ^** Department of Nephrology, The Johns Hopkins University, Baltimore, Maryland 21205, the Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, and the ^|| Institute of Bioinformatics, International Technology Park Ltd., Bangalore 560 066, India

The vascular compartment is an easily accessible compartment that provides an opportunity to measure analytes for diagnostic, prognostic, or therapeutic indications. Both serum and plasma have been analyzed extensively by proteomic approaches in an effort to catalog all proteins and polypeptides. Limitations of such approaches in obtaining a comprehensive catalog of proteins include the fact that a handful of proteins constitute over 90% of plasma protein content and that the renal glomeruli filter out proteins and polypeptides that are smaller than 66 kDa from blood. We chose to study hemodialysis fluid because it contains a higher concentration of small proteins and polypeptides and is also simultaneously depleted of the most abundant proteins present in blood. Using gel electrophoresis in combination with LC-MS/MS, we identified 292 proteins of which greater than 70% had not been previously identified from serum or plasma. More than half of the proteins identified from the hemodialysis fluid were smaller than 40 kDa. We also found 50 N-terminally acetylated peptides that allowed us to unambiguously map the N termini of mature forms of the corresponding proteins. Several identified proteins, including cytokines, were only present as predicted transcripts in data bases and thus represent novel proteins. The proteins identified in this study could serve as biomarkers in serum using more sensitive methods such as ELISA-specific antibodies.

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