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

## Documentation for package ‘MSstatsLiP’ version 1.0.0

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

## Help Pages

annotSite | Annotate modification site
BarcodePlotLiP | Barcode plot. Shows protein coverge of LiP modified peptides.
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.
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 | MSstatsLiP: A package for identifying and analyzing changes in protein structures caused by compound binding in cellur lysates.
MSstatsLiP_data | MSstatsLiP_data
MSstatsLiP_model | MSstatsLiP_model
MSstatsLiP_Summarized | MSstatsLiP_Summarized
PCAPlotLiP | Visualize PCA analysis for LiP and TrP datasets.
SkylineTest | SkylineTest
SkylinetoMSstatsLiPFormat | Converts raw LiP MS data from Skyline into the format needed for MSstatsLiP.
SpectronauttoMSstatsLiPFormat | Converts raw LiP MS data from Spectronautt into the format needed for MSstatsLiP.
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.