(c) Sam Siljee Created July 18th 2022
- Please download and install R and R studio
- Open the file "Launch_application_here.R" in RStudio
- Click on "Run App" at top right of the editor in RStudio
- Work your way through the app
- Enjoy!
- The first time you launch the app it may take some time to install all of the required packages
- The current stable version should be in the main branch
- The dev branch is what I'm currently working on, and may not be functional
- Please email samsiljee@gmail.com for help or suggestions, or submit through Github
- This is currently under development
- Import results from Proteome Discoverer or Max Quant - as PSMs, for both DDA or TMT methodologies
- Review potential contaminants
- QC plots; chromatograms
- summarisation, normalisation, and quantification in
MSstats - Perform differential abundance analysis with
MSstats, more appropriate as designed specifically for MS proteomics - Histogram of log2 foldchanges
- Perform PCA analysis, and plot clusters
- Create a heatmap of samples vs proteins
- Volcano plots of differentially abundant proteins
- GO and KEGG term analysis
- Network analysis through STRING?
- Use COPF analysis to infer proteoform differences: https://www.nature.com/articles/s41467-021-24030-x#code-availability
- Import results from Proteome Discoverer or Max Quant
- Quantify phosphopeptide enrichment
- Review potential contaminants
- Normalise in
MSstats - Search IDs against basal cell markers, and ciliated markers as a control
- Present QC data in graphs suitable for supplementary materials
- Present data tables in formats such as crosstalk (can be done with R markdown, see https://www.youtube.com/watch?v=WkF7nqEYF1E https://github.com/jthomasmock/penguin-project)
- GO annotations
- Enrichment analysis
- Biological network analysis
- Good overview of different types of analyses to try here: http://bioinformatics.sdstate.edu/go/
- LFQ Analyst: https://analyst-suite.monash-proteomics.cloud.edu.au/apps/lfq-analyst/
- Good resource on visualising enrichment analysis: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html
- ShinyGo: http://bioinformatics.sdstate.edu/go/
- QC section
- sample correlation
- Sample CVs
- Protein numbers
- Sample coverage
- Missing values heatmap
- Imputation
- See https://github.com/samsiljee/Graphing/blob/main/MS_QC/PD_QC.Rmd for other potential plots
- Better progress bars for slow processes
- Add reset to comparison matrix
- Go term analysis with complete tabular output in the analysis tab, and plots intergrated into the visualisation tab
- Pathview analysis
- Add in link to STRING website to view pathway, or embed the interactive network
- Refine selection methods for including string nodes, currently it just takes the top n most significant nodes, regardless of actual significance.
- Add WGCNA to analysis section
- Add option to use/see example data, could use MSstats test data for this perhaps
- Help text for various settings
- Create a manual?
- Fix issue with modelQC not downloading (for TMT at least) - Currently this is only a placeholder for MSstatsTMT and will not be available
- filter out infinite fold change broken
- Add ability to upload annotations and raw PSMs in multiple files
- Spell out direction A vs B say in comparison
- Fix error with update required when changing to heatmap
- Fix GO analysis and STRING
- Question mark button for description of settings
- Function to generate a R script to replicate the analysis
- Add ability to upload reference FASTA database to use as background for STRING analysis
Feel free to use this code as you wish under the MIT license, however an acknowledgement would be nice. Thanks!