friendethan / lipidmigration_ims

R codes for plotting heatmap and line plots for MALDI TOF MS data from sublimated liver tissue. Uses MALDIquant and ggplot2

Visualizing Species Migration in Sublimated Matrix for MALDI-IMS

This is an archive for the R codes used to plot the heatmaps and line charts for the MALDI-TOF IMS results included in the publication listed below. The goal of this project was to characterize the degree of vertical migration of species from the samples into the matrix layer post sublimation. Multiple spectra were obtained on the same spot in order to obtain a profile of the species present at different depths of the matrix down to the tissue layer.

Data Format

The data analyzed are obtained from the Bruker Ultraflex system with flexControl 3.4 and quadratic calibration. Multiple spectra were obtained on the same point with the same filename. As such, within one folder, there is a subfolder of the spot coordinate and within that, a list of folders numbered in the order the spectra were acquired. This allowed for correlation between folder number and sampling depth.

Files

• heatmap.R contains the script for generating the heatmap
• lineplot.R contains the script for generating the lineplots
• functions.R contains functions Ethan wrote for this project

Reference Publication

Van Nuffel S, Elie N, Yang E, Nouet J, Touboul D, Chaurand P, Brunelle A. Insights into the MALDI Process after Matrix Deposition by Sublimation Using 3D ToF-SIMS Imaging. Anal Chem. 2018 Feb 6;90(3):1907-1914. doi:10.1021/acs.analchem.7b03993 PMID: 29295614.

Contributors

• Ethan Yang: Wrote 100% of the R codes for exporting and analyzing the IMS data currently available in this repository
• Pierre Chaurand: Provided guidance and outlined the data analysis pipeline; corrected figures

Dependencies

• MALDIquant and MALDIquantForeign for obtaining the peak intensities and reading the Bruker fid data
• ggplot2 for producing the figures

Disclaimer

This repository contains only the scripts and functions for analyzing the imaging mass spectrometry data, not the SIMS-TOF data also included in the publication. The session info provided below were determined post publication and therefore may not be an accurate representation of the actual R enviornment during data analysis. The scripts provided only contains the necessary codes to produce the plots shown in the data and may need to be adapted for generic applications. It has also been scraped to remove any personal identifying information.

License

Please reference the LICENSE document for details.

Session Info

R Studio: Version Unknown
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

attached base packages:

• stats
• graphics
• grDevices
• utils
• datasets
• methods
• base

other attached packages:

• MALDIquant_1.17
• ggplot2_2.2.1

loaded via a namespace (and not attached):

• Rcpp_0.12.16
• BiocGenerics_0.24.0
• MASS_7.3-49
• munsell_0.4.3
• colorspace_1.3-2
• lattice_0.20-35
• R6_2.2.2
• rlang_0.2.0
• plyr_1.8.4
• tools_3.4.4
• parallel_3.4.4
• grid_3.4.4
• Biobase_2.38.0
• gtable_0.2.0
• irlba_2.3.2
• ProtGenerics_1.10.0
• lazyeval_0.2.1
• yaml_2.1.19
• mmand_1.5.3
• tibble_1.4.2
• Matrix_1.2-12
• Cardinal_1.2.1
• signal_0.7-6
• sp_1.2-7
• pillar_1.2.1
• compiler_3.4.4
• scales_0.5.0
• XML_3.98-1.10
• stats4_3.4.4