How to extract relevant mass spectrometry features from the different raw acquisition files ?
At the end of the course, you will understand :
- the different extraction steps
- how the parameters impact the resulting matrix
- Knowledge in liquid chromatograhy and mass spectrometry.
- You know what is the retention time.
- You know what is the ratio mass upon charge
- Presentation of xcms software
- What type of data are available in the LCMS files.
- How is build an extract ion chromatogram.
- First step : parallel extraction of ions in the different files
- Grouping step : alignment among all files
- Retention time correction step
- Replacing missing data, fillpeaks step.
- datamatrix creation step with CAMERA annotation
Summary of the key parameters defined at the differents extraction steps.
Bioconductor : opensource softaware for bioinformatics. (2018). Software packages : xcms (3.7). Repéré à http://bioconductor.org/packages/release/bioc/html/xcms.html
Smith, C. A., Want, E.J., O’Maille, G., Abagyan, R., Siuzdak, G. (2006). XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. Analytical Chemistry, 78 (3), 779–787. https://doi.org/10.1021/ac051437y