Tools for the analysis of MSP-MS data

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Documentation for package ‘mspms’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.
calculate_all_cleavages	calculate_all_cleavages calculate all possible cleavages for a defined peptide library containing peptides of the same length.
check_file_is_valid_fragpipe	check_file_is_valid_fragpipe Check to make sure the input data looks like the expected FragPipe file.
check_file_is_valid_pd	check_file_is_valid_pd Check to make sure the input data looks like the expected ProteomeDiscoverer file.
colData	colData A tibble containing the colData associated with an experiment to proc
generate_report	generate_report
limma_stats	limma_stats
log2fc_t_test	log2fc_t_test
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	mspms_tidy Convert a SummarizedExperiment object within a QFeatures object into a tidy tibble.
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
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_qc_check plot the the percentage of the peptide library undetected in each sample per each sample group.
plot_time_course	plot_time_course
plot_volcano	plot_volcano
prepare_fragpipe	prepare_fragpipe
prepare_pd	prepare_pd Prepare a label free quantification file exported from Proteome Discoverer for subsequent mspms analysis.
prepare_peaks	prepare_peaks Prepare a label free quantification file exported from PEAKS for subsequent mspms analysis.
processed_qf	processed_qf A QFeatures object prepared from PEAKS data of Cathepsin data that has been processed (imputation/normalization)
process_qf	process_qf