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Proteome profiling of human cerebrospinal fluid: exploring the potential of capillary electrophoresis with surface modified capillaries for analysis of complex biological samples.

Journal article
Authors Aida Zuberovic
Jörg Hanrieder
Ulf Hellman
Jonas Bergquist
Magnus Wetterhall
Published in European journal of mass spectrometry (Chichester, England)
Volume 14
Issue 4
Pages 249-60
ISSN 1469-0667
Publication year 2008
Published at Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry
Pages 249-60
Language en
Keywords Adolescent, Adult, Aged, Amino Acid Sequence, Biomarkers, cerebrospinal fluid, Cerebrospinal Fluid, chemistry, Electrophoresis, Capillary, instrumentation, methods, Humans, Middle Aged, Molecular Sequence Data, Peptides, cerebrospinal fluid, chemistry, Protein Array Analysis, instrumentation, methods, Proteomics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, methods, Tandem Mass Spectrometry
Subject categories Analytical Chemistry, Neurochemistry


A bottom-up proteomic approach, based on capillary electrophoresis (CE) in combination with matrix- assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-ToF/ToF MS), was used to analyze immunoaffinity depleted human cerebrospinal fluid (CSF) and compare it with a non-depleted sample. After enzymatic digestion and desalting, the tryptic peptides were separated by CE using PolyE-323 modified capillaries and fractionated off-line onto MALDI target plates for further analysis by MALDI-MS and MS/MS. The protein profile of the depleted sample was compared with non depleted CSF. Overall, 85 proteins were identified with 95% significance in both samples. The significance scores for proposed biomarkers, such as amyloid-like protein 1 precursor, could be increased up to 12 times after the depletion. Other proteins, often suggested to be related to neurodegenerative diseases, like amyloid beta A4 protein precursor, superoxide dismutase and apolipoprotein E precursor could only be found in the depleted CSF samples. The effect of a derivatization of tryptic peptides with 2- methoxy-4,5-dihydro-1H-imidazole reagent for protein identification with MS was also employed to increase the number of identified proteins and the sequence coverages. The results presented in this study illustrate the benefit of combining a sample pre-fractionation step and a label's ability to enhance the ionization efficiency with the potential of CE using PolyE-323 modified capillaries in the analysis of complex samples. The straight-forward approach that provides speed and simplicity resulting in high-resolution separations and low sample consumption represents an easily applicable separation technique that can serve as a complement to other currently existing analytical approaches needed in modern proteomic analysis of clinically relevant samples.

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