Metabolomics
From BITS wiki
Contents
Slides
Exercises
- Exercise 1 Converting raw data from vendor format to open format (mzML) using msconvert tool of ProteoWizard
- Exercise 2 Processing data: peak picking and peak matching
Convert files to mzML format using msconvert of ProteoWizard (see exercise 1)
Analyze the data in R/RStudio using the xcms package - Exercise 3
- Exercise 4
- Exercise 5
Files
MS spectral library: take file GMD_20111121_MDN35_ALK_MSL.txt
Software
Bioconductor and Bioconductor packages
- Bioconductor
- xcms for data processing
- IPO to optimize the processing parameters of xcms
- CAMERA to group peaks of ions of the same compound (peaks with equal elution time)
- mz.unity further examination of CAMERA results
- credential to remove contaminating peaks
Other software
- ProteoWizard for file conversion
- AMDIS for peak identification
- CSI:FingerID