title: Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis.
abstract: The aims of the study were to: (i) identify differentially regulated proteins in cerebrospinal fluid (CSF) between multiple sclerosis (MS) patients and non-MS controls; (ii) examine the effect of matching the CSF samples on either total protein amount or volume, and compare four protein normalization strategies for CSF protein quantification. CSF from MS patients (n = 37) and controls (n = 64), consisting of other noninflammatory neurological diseases (n = 50) and non neurological spinal anesthetic subjects (n = 14), were analyzed using label-free proteomics, quantifying almost 800 proteins. In total, 122 proteins were significantly regulated (p < 0.05), where 77 proteins had p-value <0.01 or AUC value >0.75. Hierarchical clustering indicated that there were two main groups of MS patients, those with increased levels of inflammatory response proteins and decreased levels of proteins involved in neuronal tissue development (n = 30), and those with normal protein levels for both of these protein groups (n = 7). The main subgroup of controls clustering with the MS patients showing increased inflammation and decreased neuronal tissue development were patients suffering from chronic fatigue. Our data indicate that the preferable way to quantify proteins in CSF is to first match the samples on total protein amount and then normalize the data based on the median intensities, preferably from the CNS-enriched proteins.
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.|The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors: Jill A
authors: JA
authors: Opsahl
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.
authors: Marc
authors: M
authors: Vaudel
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.|The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors: Astrid
authors: A
authors: Guldbrandsen
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.
authors: Elise
authors: E
authors: Aasebø
authors: Neurology Department, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium.
authors: Vincent
authors: V
authors: Van Pesch
authors: Laboratory of Neuroimmunology, IRCCS, "C. Mondino" National Neurological Institute, Pavia, Italy.
authors: Diego
authors: D
authors: Franciotta
authors: The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors: Kjell-Morten
authors: KM
authors: Myhr
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.|Department of Clinical Science, University of Bergen, Bergen, Norway.
authors: Harald
authors: H
authors: Barsnes
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.|Surgical Clinic, Haukeland University Hospital, Bergen, Norway.
authors: Magnus
authors: M
authors: Berle
authors: The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.|The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
authors: Øivind
authors: Ø
authors: Torkildsen
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.|The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors: Ann C
authors: AC
authors: Kroksveen
authors: Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.|The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
authors: Frode S
authors: FS
authors: Berven
mesh_terms: D002556:Cerebrospinal Fluid Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D016000:Cluster Analysis; D006801:Humans; D009103:Multiple Sclerosis / Q000378:metabolism*; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics / Q000379:methods* / Q000592:standards
chemical_list: D002556:Cerebrospinal Fluid Proteins; D020543:Proteome
keywords: Biomarker; Biomedicine; Inflammation; Label free; Multiple sclerosis; Neurodegeneration