MSstatsLiP {MSstatsLiP} | R Documentation

## MSstatsLiP: A package for identifying and analyzing changes in protein structures caused by compound binding in cellur lysates.

### Description

A set of tools for detecting differentially abundant LiP peptides in shotgun mass spectrometry-based proteomic experiments. The package includes tools to convert raw data from different spectral processing tools, summarize feature intensities, and fit a linear mixed effects model. If overall protein abundance changes are included, the package will also adjust the LiP peptide fold change for changes in overall protein abundace. Additionally the package includes functionality to plot a variety of data visualizations.

### functions

- `SpectronauttoMSstatsLiPFormat` : Generates MSstatsLiP required input format for Spectronaut outputs.

- `trypticHistogramLiP` : Histogram of Half vs Fully tryptic peptides. Calculates proteotypicity, and then uses calcualtions in histogram.

- `correlationPlotLiP` : Plot run correlation for provided LiP and TrP experiment.

- `dataSummarizationLiP` : Summarizes PSM level quantification to peptide (LiP) and protein level quantification.

- `dataProcessPlotsLiP` : Visualization for explanatory data analysis. Specifically gives ability to plot Profile and Quality Control plots.

- `PCAPlotLiP` :Visualize PCA analysis for LiP and TrP datasets. Specifically gives ability to plot explanined varaince per component, Protein/Peptide PCA, and Condition PCA.

- `groupComparisonLiP` : Tests for significant changes in LiP and protein abundance across conditions. Adjusts LiP fold change for changes in protein abundance.

- `groupComparisonPlotsLiP` : Visualization for model-based analysis and summarization.

- `PCAPlotLiP` : Runs PCA on the summarized data. Can visualize the PCA analysis in three different plots.

- `BarcodePlotLiP` : Shows protein coverage of LiP modified peptides. Shows significant, insignificant, and missing coverage.

[Package MSstatsLiP version 1.0.0 Index]