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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manual.pdf |manual.html✨
card.svg |card.png
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-1.5.0(bioc 3.24)mspms-1.4.0(bioc 3.23)

proteomicsmassspectrometrypreprocessingproteaseproteomics-data-analysis

4.00 score 1 stars 7 scripts 256 downloads 21 exports 176 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksNOTE200
linux-devel-x86_64OK572
source / vignettesOK333
linux-release-x86_64OK549
macos-release-arm64OK295
macos-oldrel-arm64OK389
windows-develOK539
windows-releaseOK510
windows-oldrelOK441
wasm-releaseOK238

Exports:%>%calculate_all_cleavagesgenerate_reportlimma_statslog2fc_t_testmspms_tidyplot_all_icelogosplot_cleavages_per_posplot_heatmapplot_icelogoplot_nd_peptidesplot_pcaplot_qc_checkplot_time_courseplot_volcanoprepare_diannprepare_fragpipeprepare_pdprepare_peaksprepare_sageprocess_qf

Dependencies:abindAnnotationFilteraskpassassertthatbackportsbase64encBiobaseBiocBaseUtilsBiocGenericsbitbit64bootbroombslibcacachemcallrcarcarDataclicliprclueclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydendextendDerivdigestdoBydplyreggevaluatefarverfastmapfontawesomeforeachforecastFormulafracdifffsgclusgenericsGenomicRangesggplot2ggpubrggrepelggsciggseqlogoggsignifgluegmmgridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttrigraphimputeimputeLCMDIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelimmalme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMsCoreUtilsMultiAssayExperimentmvtnormnlmenloptrnnetnormnumDerivopensslotelpbkrtestpcaMethodspermutepillarpkgconfigplotlyplyrpolynomprettyunitsprocessxprogresspromisesProtGenericspspurrrqapQFeaturesquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasregistryreshape2rlangrmarkdownrstatixS4ArraysS4VectorsS7sandwichsassscalesSeqinfoseriationSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetinytextmvtnormTSPtzdburcautf8vctrsveganviridisviridisLitevroomwebshotwithrxfunXVectoryamlzoo

mspms_vignette

Rendered frommspms_vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-11-12
Started: 2024-09-26

Readme and manuals

Help Manual

Help pageTopics
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 proccolData
generate_reportgenerate_report
limma_statslimma_stats
log2fc_t_testlog2fc_t_test
log2fc_t_test_data A tibble containing the results of t-tests and log2fc compared to time 0 14,497 × 19log2fc_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 objectmspms_tidy_data
peaks_prepared_data A QFeatures object prepared from PEAKS data of cathepsin data/.peaks_prepared_data
peptide_librarypeptide_library
plot_all_icelogosplot_all_icelogos
plot_cleavages_per_posplot_cleavages_per_pos
plot_heatmapplot_heatmap
plot_icelogoplot_icelogo
plot_nd_peptidesplot_nd_peptides
plot_pcaplot_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_courseplot_time_course
plot_volcanoplot_volcano
prepare_diannprepare_diann
prepare_fragpipeprepare_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 analysisprepare_peaks
prepare_sage Prepare a label free quantification file exported from Sage for subsequent mspms analysis.prepare_sage
process_qfprocess_qf
processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed (imputation/normalization)processed_qf