Package: mspms 0.99.7

Charlie Bayne

mspms: Tools for the analysis of MSP-MS data

This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.

Authors:Charlie Bayne [aut, cre]

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mspms.pdf |mspms.html✨
mspms/json (API)
NEWS

# Install 'mspms' in R:

install.packages('mspms', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/baynec2/mspms/issues

Datasets:

all_possible_8mers_from_228_library - All_possible_8mers_from_228_library All possible 8mers from the standard (as of 26April2024) 228 MSP-MS peptide library (This is equivalent to the result of mspms::calculate_all_cleavages(mspms::peptide_library$real_cleavage_seq,n=4)) vector of the 14 AA peptides used in the library.
colData - ColData A tibble containing the colData associated with an experiment to proc
log2fc_t_test_data - Log2fc_t_test_data A tibble containing the results of t-tests and log2fc compared to time 0 14,497 × 19
mspms_tidy_data - Mspms_tidy_data A tibble containing tidy data derived from QFeatures object
peaks_prepared_data - Peaks_prepared_data A QFeatures object prepared from PEAKS data of cathepsin data/.
peptide_library - Peptide_library
processed_qf - Processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed

On BioConductor:mspms-0.99.6(bioc 3.21)

proteomics massspectrometry preprocessing protease proteomics-data-analysis

4.95 score 4 scripts 18 exports 159 dependencies

Last updated 26 days agofrom:9653326c74. Checks:OK: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 03 2024
R-4.5-win	OK	Dec 03 2024
R-4.5-linux	OK	Dec 03 2024
R-4.4-win	OK	Dec 03 2024
R-4.4-mac	OK	Dec 03 2024

Exports:%>%calculate_all_cleavages generate_report log2fc_t_test mspms_tidy plot_all_icelogos plot_cleavages_per_pos plot_heatmap plot_icelogo plot_nd_peptides plot_pca plot_qc_check plot_time_course plot_volcano prepare_fragpipe prepare_pd prepare_peaks process_qf

Dependencies:abind AnnotationFilter askpass assertthat backports base64enc Biobase BiocBaseUtils BiocGenerics bit bit64 boot broom bslib ca cachem callr car carData cli clipr clue cluster codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl data.table DelayedArray dendextend Deriv digest doBy dplyr egg evaluate fansi farver fastmap fontawesome foreach Formula fs gclus generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggpubr ggrepel ggsci ggseqlogo ggsignif glue gridExtra gtable heatmaply highr hms htmltools htmlwidgets httr igraph IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr MsCoreUtils MultiAssayExperiment munsell nlme nloptr nnet numDeriv openssl pbkrtest permute pillar pkgconfig plotly plyr polynom prettyunits processx progress promises ProtGenerics ps purrr qap QFeatures quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen readr registry reshape2 rlang rmarkdown rstatix S4Arrays S4Vectors sass scales seriation SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex TSP tzdb UCSC.utils utf8 vctrs vegan viridis viridisLite vroom webshot withr xfun XVector yaml zlibbioc

mspms_vignette

Rendered frommspms_vignette.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-11-21
Started: 2024-09-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
all_possible_8mers_from_228_library All possible 8mers from the standard (as of 26April2024) 228 MSP-MS peptide library (This is equivalent to the result of mspms::calculate_all_cleavages(mspms::peptide_library$real_cleavage_seq,n=4)) vector of the 14 AA peptides used in the library.	all_possible_8mers_from_228_library
calculate_all_cleavages calculate all possible cleavages for a defined peptide library containing peptides of the same length.	calculate_all_cleavages
check_file_is_valid_fragpipe Check to make sure the input data looks like the expected FragPipe file.	check_file_is_valid_fragpipe
check_file_is_valid_pd Check to make sure the input data looks like the expected ProteomeDiscoverer file.	check_file_is_valid_pd
colData A tibble containing the colData associated with an experiment to proc	colData
generate_report	generate_report
log2fc_t_test	log2fc_t_test
log2fc_t_test_data A tibble containing the results of t-tests and log2fc compared to time 0 14,497 × 19	log2fc_t_test_data
mspms_tidy Convert a SummarizedExperiment object within a QFeatures object into a tidy tibble.	mspms_tidy
mspms_tidy_data A tibble containing tidy data derived from QFeatures object	mspms_tidy_data
peaks_prepared_data A QFeatures object prepared from PEAKS data of cathepsin data/.	peaks_prepared_data
peptide_library	peptide_library
plot_all_icelogos	plot_all_icelogos
plot_cleavages_per_pos	plot_cleavages_per_pos
plot_heatmap	plot_heatmap
plot_icelogo	plot_icelogo
plot_nd_peptides	plot_nd_peptides
plot_pca	plot_pca
plot_qc_check plot the the percentage of the peptide library undetected in each sample per each sample group.	plot_qc_check
plot_time_course	plot_time_course
plot_volcano	plot_volcano
prepare_fragpipe	prepare_fragpipe
prepare_pd Prepare a label free quantification file exported from Proteome Discoverer for subsequent mspms analysis.	prepare_pd
prepare_peaks Prepare a label free quantification file exported from PEAKS for subsequent mspms analysis.	prepare_peaks
process_qf	process_qf
processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed (imputation/normalization)	processed_qf