# Tools for the analysis of MSP-MS data

## Documentation for package ‘mspms’ version 1.3.1

- 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_diann | check_file_is_valid_diann Check to make sure the input data looks like the expected DIA-NN output file.
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_diann | prepare_diann
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 label-free quantification data for MSP-MS analysis
prepare_sage | prepare_sage Prepare a label free quantification file exported from Sage 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