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Background  Neurologic Post Treatment Lyme disease ( nPTLS ) and Chronic Fatigue ( CFS ) are syndromes of unknown etiology. They share features of fatigue and cognitive dysfunction, making it difficult to differentiate them. Unresolved is whether  nPTLS  is a subset of  CFS .    Methods and Principal Findings  Pooled cerebrospinal fluid (CSF) samples from  nPTLS patients ,  CFS  patients, and healthy volunteers were comprehensively analyzed using high-resolution mass spectrometry (MS), coupled with immunoaffinity depletion methods to reduce protein-masking by abundant proteins. Individual patient and healthy control CSF samples were analyzed directly employing a MS-based label-free quantitative proteomics approach. We found that both groups, and individuals within the groups, could be distinguished from each other and normals based on their specific CSF proteins (p<0.01).  CFS  (n = 43) had 2,783 non-redundant proteins,  nPTLS  (n = 25) contained 2,768 proteins, and healthy normals had 2,630 proteins. Preliminary pathway analysis demonstrated that the data could be useful for hypothesis generation on the pathogenetic mechanisms underlying these two related syndromes.    Conclusions    nPTLS  and  CFS  have distinguishing CSF protein complements. Each condition has a number of CSF proteins that can be useful in providing candidates for future validation studies and insights on the respective mechanisms of pathogenesis. Distinguishing  nPTLS  and  CFS  permits more focused study of each condition, and can lead to novel diagnostics and therapeutic interventions.

Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome