Computational protocol: Annotation of the human cerebrospinal fluid lipidome using high resolution mass spectrometry and a dedicated data processing workflow

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Protocol publication

[…] Raw files were first of all converted to mzXML format with MSconvert (ProteoWizard). Peak detection, alignment and integration were performed with the XCMS software package version 1.30.3 (Smith et al. ) including the CentWave algorithm (Tautenhahn et al. ). The list of the parameters used is available as supplementary material (see Table S2 provided as supplementary material). A data matrix was generated by the software. It contained the list of all detected features, including information such as accurate measured masses, retention times and areas of chromatographic peaks. […]

Pipeline specifications

Software tools ProteoWizard, XCMS
Application MS-based untargeted proteomics
Organisms Homo sapiens
Diseases Multiple Sclerosis, Nervous System Diseases
Chemicals Fatty Acids, Sphingolipids