In Pohnert-Lab/DeltaMS: Isotopologue finder

File preparation

Slicing thermo raw files which have been recorded using the polarity switching methods.

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

1. Get the raw file slicer from your Thermo distributor
2. Install according to the requirements
3. Open Xcalibur QualBrowser
4. Click on top toolbar “Tools” (1) and then select the “Slicer” (2)
5. Select your “Input”(3) file and the “Output” file (4)
6. Select the “Scan filter” which you like to export (5)
7. Click on “Create New File”(6)

File conversion of thermo raw files using the thermo file converter

1. Open Xcalibur
2. Click on top toolbar "Tools" (1) and then select the "File converter" (2)
3. Select your "Source data type" (3) and the folder where the data resides by using the "Browse..." button (4).
4. Select the file you like to convert and choose the "Destination data type:" as ANDI files *.cdf. (5)
5. Finally click on "Add Job(s)" (7) and "Convert" (8)

File conversion using proteowizard (Chambers et al. 2012)

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.

Installation of programs

Requirements:

• An internet browser eg. Firefox
• Java (for rJava) https://www.java.com/
• Adobe reader or related program

Installing DeltaMS

1. Install missing packages using following function:

MissingPackagesDeltaMS()

1. X13CMS (Huang et al. 2014) is required a) Download X13CMS tar.gz file from the Patti lab homepage b) Install the package as the DeltaMS package was installed.

Working with DeltaMS

Starting DeltaMS

Type in your console:

library(DeltaMS) RunDeltaMS()

Closing DeltaMS

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())

Locating DeltaMS save files

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()

Folder structure

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

• WD
• MS files

Dataset comparison

• WD
• labeled data
  • MS files
• unlabeled data
  • MS files

Isotopologue-guided perturbation analysis

• WD
• labeled control
  • MS files
• unlabeled control
  • MS files
• labeled treatment
  • MS files
• unlabeled treatment
  • MS files

DeltaMS 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.

References

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.

Pohnert-Lab/DeltaMS documentation built on Jan. 4, 2021, 12:49 p.m.