# LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

## Documentation for package ‘MSstatsLiP’ version 1.18.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

annotSite | Annotate modification site
calculateProteolyticResistance | Calcutates proteolytic resistance for provided data. Requires input from dataSummarizationLiP function. Can optionally calculate differential analysis using proteolytic resistance. In order for this function to work, Conditions and run numbers must match between the LiP and TrP data.
calculateTrypticity | Calculates level of trypticity for a list of LiP Peptides.
correlationPlotLiP | Plot run correlation for provided LiP and TrP experiment.
dataProcessPlotsLiP | Visualization for explanatory data analysis
dataSummarizationLiP | Summarizes LiP and TrP datasets seperately using methods from MSstats.
DIANNtoMSstatsLiPFormat | Converts raw LiP MS data from DIA-NN into the format needed for MSstatsLiP.
groupComparisonLiP | Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasets
groupComparisonPlotsLiP | Visualization for model-based analysis and summarization
LiPRawData | LiPRawData
locateMod | Locate modified sites with a peptide
locatePTM | Annotate modified sites with associated peptides
MSstatsLiP_data | MSstatsLiP_data
MSstatsLiP_model | MSstatsLiP_model
MSstatsLiP_Summarized | MSstatsLiP_Summarized
PCAPlotLiP | Visualize PCA analysis for LiP and TrP datasets.
raw_lip | raw_lip
raw_prot | raw_prot
ResistanceBarcodePlotLiP | Proteolytic Resistance Barcode plot. Shows accessibility score of different fully tryptic peptides in a protein.
SkylineTest | SkylineTest
SkylinetoMSstatsLiPFormat | Converts raw LiP MS data from Skyline into the format needed for MSstatsLiP.
SpectronauttoMSstatsLiPFormat | Converts raw LiP MS data from Spectronaut into the format needed for MSstatsLiP.
StructuralBarcodePlotLiP | Barcode plot. Shows protein coverge of LiP modified peptides.
tidyFasta | Read and tidy a FASTA file
TrPRawData | TrPRawData
trypticHistogramLiP | Histogram of Half vs Fully tryptic peptides. Calculates proteotypicity, and then uses calcualtions in histogram.