Package: mspms 1.5.0

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]

mspms_1.5.0.tar.gz
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mspms_1.5.0.tgz(r-4.6-any)mspms_1.5.0.tgz(r-4.5-any)
mspms_1.5.0.tar.gz(r-4.7-any)mspms_1.5.0.tar.gz(r-4.6-any)
mspms_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mspms/json (API)

# 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-1.5.0(bioc 3.24)mspms-1.4.0(bioc 3.23)

proteomics massspectrometry preprocessing protease proteomics-data-analysis

4.00 score 1 stars 7 scripts 285 downloads 21 exports 175 dependencies

Last updated from:e9f2f9604c. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	232
linux-devel-x86_64	OK	484
source / vignettes	OK	342
linux-release-x86_64	OK	540
macos-release-arm64	OK	268
macos-oldrel-arm64	OK	251
windows-devel	OK	422
windows-release	OK	467
windows-oldrel	OK	305
wasm-release	OK	173

Exports:%>%calculate_all_cleavages generate_report limma_stats 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_diann prepare_fragpipe prepare_pd prepare_peaks prepare_sage 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 farver fastmap fontawesome foreach forecast Formula fracdiff fs gclus generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggseqlogo ggsignif glue gmm gridExtra gtable heatmaply highr hms htmltools htmlwidgets httr igraph impute imputeLCMD IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle limma lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr MsCoreUtils MultiAssayExperiment mvtnorm nlme nloptr nnet norm numDeriv openssl otel pbkrtest pcaMethods permute pillar pkgconfig plotly plyr polynom prettyunits processx progress promises ProtGenerics ps purrr qap QFeatures quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas registry reshape2 rlang rmarkdown rstatix S4Arrays S4Vectors S7 sandwich sass scales Seqinfo seriation SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex tmvtnorm TSP tzdb urca utf8 vctrs vegan viridis viridisLite vroom webshot withr xfun XVector yaml zoo

mspms_vignette

Rendered frommspms_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-11-12
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_diann Check to make sure the input data looks like the expected DIA-NN output file.	check_file_is_valid_diann
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
limma_stats	limma_stats
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_diann	prepare_diann
prepare_fragpipe	prepare_fragpipe
prepare_pd Prepare a label free quantification file exported from Proteome Discoverer for subsequent mspms analysis.	prepare_pd
Prepare PEAKS label-free quantification data for MSP-MS analysis	prepare_peaks
prepare_sage Prepare a label free quantification file exported from Sage for subsequent mspms analysis.	prepare_sage
process_qf	process_qf
processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed (imputation/normalization)	processed_qf