Establishing the proteome of normal human cerebrospinal fluid

Abstract

Background: Knowledge of the entire protein content, the proteome, of normal human cerebrospinal fluid (CSF) would enable insights into neurologic and psychiatric disorders. Until now technologic hurdles and access to true normal samples hindered attaining this goal.

Methods and principal findings: We applied immunoaffinity separation and high sensitivity and resolution liquid chromatography-mass spectrometry to examine CSF from healthy normal individuals. 2630 proteins in CSF from normal subjects were identified, of which 56% were CSF-specific, not found in the much larger set of 3654 proteins we have identified in plasma. We also examined CSF from groups of subjects previously examined by others as surrogates for normals where neurologic symptoms warranted a lumbar puncture but where clinical laboratory were reported as normal. We found statistically significant differences between their CSF proteins and our non-neurological normals. We also examined CSF from 10 volunteer subjects who had lumbar punctures at least 4 weeks apart and found that there was little variability in CSF proteins in an individual as compared to subject to subject.

Conclusions: Our results represent the most comprehensive characterization of true normal CSF to date. This normal CSF proteome establishes a comparative standard and basis for investigations into a variety of diseases with neurological and psychiatric features.

Figure 1. Venn diagram showing the amount of overlap of our dataset with a comparable dataset of proteins detected in the CSF of “normal clinical value” or “neurologic surrogate-normal” individuals who required a lumbar puncture for clinical reasons as reported by Zougman et al.

The large circle represents the 2630 proteins observed in our comprehensive dataset of proteins detected in the CSF of normal individuals. The small circle represents the 798 proteins identified in the analysis by Zougman et al.

Figure 2. Unsupervised hierarchical clustering of all proteins identified and quantified in direct LC-MS analyses of CSF samples from 10 normal healthy individuals (5 males and 5 females; 37–44 years old; each has two longitudinal samples collected at least 4 weeks apart).

Log2 transformed protein abundances were used. M: male; F: female; numbers right after the hyphen indicate the two serial samples from the same individual.

Figure 3. Unsupervised hierarchical clustering of all proteins identified and quantified in direct replicate LC-MS analyses of pooled CSF from non-neurologic surrogate-normal individuals (n = 200) and neurologic surrogate-normal (headache) patients (n = 10).

Log2 transformed protein abundances were used.