If data are recorded using polarity switching methods the files have to be divided into a file containing the positive ionization mode data and a file
Download and install the latest proteowizard version from:
http://proteowizard.sourceforge.net/
Run the program using the following settings:
https://xcmsonline.scripps.edu/docs/fileformats.html
NOTE: If the command line version of proteowizard is used the polarity separation (slicing) from e.g. Thermo raw files can be made directly there.
MissingPackagesDeltaMS()
Type in your console:
library(DeltaMS)
RunDeltaMS()
Close the browser tab and press the "Stop" button inside RStudio or press "escape" alternatively.
Note: It is recommended to clear the workspace after a performed analysis using the brush symbol in the environment or the command:
rm(list=ls())
DeltaMS saves settings as bookmarks which reside inside the “shiny_bookmarks” folder inside the DeltaMS package folder in the R package library. To share or delete a DeltaMS bookmark, the whole bookmark folder has to be used (including input.rds and values.rds files).
To get the path to the “shiny_bookmarks” folder, copy and execute this line in RStudio console:
LocateDeltaMSSettings()
The top folder that contains other folders or MS files directly is called the working directory (WD). Labeling of the folders is up to the user. For the isotope signature analysis, MS files have to be placed inside the WD.
Isotope signature
Dataset comparison
Isotopologue-guided perturbation analysis
In general, several analyses, using different settings, can be performed in a row. For every analysis, a new DeltaMS_results_date_time folder is created inside the WD.
Chambers, M. C., Maclean, B., Burke, R., Amodei, D., Ruderman, D. L., Neumann, S., et al. (2012). A cross-platform toolkit for mass spectrometry and proteomics. [Opinion and Comment]. Nat. Biotech., 30(10), 918-920, doi:10.1038/nbt.2377
http://www.nature.com/nbt/journal/v30/n10/abs/nbt.2377.html#supplementary-information.
Huang, X., Chen, Y. J., Cho, K., Nikolskiy, I., Crawford, P. A., & Patti, G. J. (2014). X13CMS: global tracking of isotopic labels in untargeted metabolomics. Anal. Chem., 86(3), 1632-1639, doi:10.1021/ac403384n.
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