friendethan / SilverSpray_IMS

Script for analyzing intensity of olefin species from AgLDI IMS data. Uses MALDIquant, Cardinal and Tidyverse

Analysis of Total Cholesterol Intensity with Imaging Mass Spectrometry

This is an archive for the R codes used in the data analysis pipeline in the publication listed below to calculate the total cholesterol intensity from imaging mass spectometry data of mouse brain homogenates following silver nitrate spray

Files

• workflow.md contains the data analysis workflow and other necessary parameters
• extractIntensity.R contains the script for exporting the mean intensity for each sample at various thicknesses
• calculateStats.R contains the script for calculating ANOVA and comparing thicknesses
• functions.R contains the functions called during the script

Reference Publication

Yang E, Fournelle F, Chaurand P. Silver spray deposition for AgLDI imaging MS of cholesterol and other olefins on thin tissue sections. J Mass Spectrom. 2020 Apr;55(4):e4428. doi:10.1002/jms.4428. Epub 2019 Aug 30. PMID: 31410898.

Contributors

• Ethan Yang: Wrote 100% of the R codes for exporting and analyzing the IMS data for the mouse brain homogenates in the publication, unless otherwise noted.
• Frédéric Fournelle: Helped with exporting figures and obtaining some of the data for the publication
• Pierre Chaurand: Provided guidance and outlined the data analysis pipeline; corrected figures

Dependencies

• Cardinal for reading MALDI imaging data
• MALDIquant and MALDIquantForeign for obtaining peak intensities and peak picking
• Tidyverse for data wrangling and summarizing after peak picking

Disclaimer

This repository contains only the scripts and functions for analyzing the entire imaging mass spectrometry data included in the publication. However, 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 have been scrapped to remove any personal identifying information.

License

Please reference the LICENSE document for details.

Session Info

RStudio: Version 1.3.959

R version: 3.4.4
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:

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

Other attached packages:

• MALDIquant_1.17
• XML_3.98-1.10
• Cardinal_1.2.1
• ProtGenerics_1.10.0
• Biobase_2.38.0
• BiocGenerics_0.24.0

loaded via a namespace (and not attached):

• Rcpp_0.12.16
• MASS_7.3-49
• lattice_0.20-35
• R6_2.2.2
• rlang_0.2.0
• tools_3.4.4
• grid_3.4.4
• irlba_2.3.2
• yaml_2.1.19
• mmand_1.5.3
• Matrix_1.2-12
• signal_0.7-6
• sp_1.2-7
• compiler_3.4.4
• stats4_3.4.4

R version: 3.6.0
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

attached base packages:

• stats4
• parallel
• stats
• graphics
• grDevices utils
• datasets
• methods
• base

other attached packages:

• forcats_0.5.0
• stringr_1.4.0
• dplyr_0.8.5
• purrr_0.3.4
• readr_1.3.1
• tidyr_0.8.3
• tibble_3.0.1
• ggplot2_3.3.0
• tidyverse_1.2.1
• MALDIquant_1.19.3
• Biobase_2.44.0
• XML_3.99-0.3
• Cardinal_2.2.5
• ProtGenerics_1.16.0
• S4Vectors_0.22.1
• EBImage_4.26.0
• BiocParallel_1.18.1
• BiocGenerics_0.30.0

loaded via a namespace (and not attached):

• httr_1.4.1
• jsonlite_1.6.1
• viridisLite_0.3.0
• modelr_0.1.4
• assertthat_0.2.1
• sp_1.3-1
• tiff_0.1-5
• cellranger_1.1.0
• yaml_2.2.0
• pillar_1.4.4
• backports_1.1.6
• lattice_0.20-38
• glue_1.4.0
• digest_0.6.25
• rvest_0.3.4
• colorspace_1.4-1
• MALDIquantForeign_0.12
• htmltools_0.4.0
• Matrix_1.2-17
• pkgconfig_2.0.3
• broom_0.5.6
• biglm_0.9-1
• haven_2.2.0
• fftwtools_0.9-8
• scales_1.1.0
• jpeg_0.1-8.1
• generics_0.0.2
• ellipsis_0.3.0
• withr_2.2.0
• cli_2.0.2
• magrittr_1.5
• crayon_1.3.4
• readxl_1.3.1
• mclust_5.4.3
• fansi_0.4.1
• nlme_3.1-139
• MASS_7.3-51.4
• xml2_1.2.0
• tools_3.6.0
• hms_0.5.3
• lifecycle_0.2.0
• munsell_0.5.0
• locfit_1.5-9.1
• irlba_2.3.3
• compiler_3.6.0
• signal_0.7-6
• rlang_0.4.6
• grid_3.6.0
• RCurl_1.95-4.12
• rstudioapi_0.11
• htmlwidgets_1.5.1
• bitops_1.0-6
• base64enc_0.1-3
• gtable_0.3.0
• abind_1.4-5
• DBI_1.1.0
• mmand_1.6.1
• R6_2.4.1
• lubridate_1.7.4
• stringi_1.4.3
• matter_1.10.0
• readMzXmlData_2.8.1
• Rcpp_1.0.4.6
• vctrs_0.2.4
• readBrukerFlexData_1.8.5
• png_0.1-7
• tidyselect_0.2.5