Human cerebrospinal fluid data for use as spectral library, for biomarker research

Lukas M Schilde; Simone Steinbach; Bettina Serschnitzki; Fabian Maass; Mathias Bähr; Paul Lingor; Katrin Marcus; Caroline May

doi:10.1016/j.dib.2020.106048

Human cerebrospinal fluid data for use as spectral library, for biomarker research

Data Brief. 2020 Jul 19:32:106048. doi: 10.1016/j.dib.2020.106048. eCollection 2020 Oct.

Authors

Lukas M Schilde^{1

2}, Simone Steinbach^{1

2}, Bettina Serschnitzki^{1

2}, Fabian Maass³, Mathias Bähr³, Paul Lingor^{3

4

5}, Katrin Marcus^{1

2}, Caroline May^{1

2}

Affiliations

¹ Ruhr-University Bochum, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Germany.
² Ruhr-University Bochum, Medical Faculty, Medizinisches Proteom-Center, Germany.
³ Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.
⁴ Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, Göttingen, Germany.
⁵ Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Department of Neurology, München, Germany.

Abstract

Spectral libraries generated by data dependent acquisition (DDA) are a useful tool for the analysis of data created by data independent acquisition (DIA) in mass spectrometry. The quality of DIA analysis is dependent on the quality of the spectral library. We used cerebrospinal fluid (CSF) of patients with Parkinson's disease and healthy controls to create a spectral library of human CSF proteome. To this date, there is no validated CSF biomarker for Parkinson's disease. This data set may therefore be valuable for the future analysis of CSF proteins. Part of the samples consisted of fractions that were separated by gel electrophoresis. After tryptic digestion, all samples were spiked with indexed retention time (iRT) peptides and were measured using a DDA mass spectrometry approach. The here provided data set can be used as a CSF-specific spectral library. Data files generated from the described workflow are hosted in the public repository ProteomeXchange under the identifier PXD013487.

Keywords: Cerebrospinal fluid; Data-independent acquisition; Mass spectrometry; Parkinson's disease; Proteomics; Spectral library.