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MSstats (version 2.6.0)

Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Description

A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.

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Version

Version

2.6.0

License

Artistic-2.0

Maintainer

Meena Choi

Last Published

February 15th, 2017

Functions in MSstats (2.6.0)

Quantitative data after data pre-processing and quality control of MS runs

groupComparison

Finding differentially abundant proteins across conditions in LC-MS, SRM and DIA experiment

groupComparisonPlots

Visualization for model-based analysis and summarizing differentially abundant proteins

testResultOneComparison

Significance testing result of one comparison between two groups

transformMSnSetToMSstats

Transforms a MSnSet class dataset into a required input for MSstats

Protein sample quantification or group quantification

designSampleSize

Planning future experimental designs of label-free and label-based LC-MS, SRM, DIA experiments in sample size calculation

designSampleSizePlots

Visualization for sample size calculation

modelBasedQCPlots

Visualization for model-based quality control in fitting model

MSstats-package

Tools for protein significance analysis in DDA,SRM and DIA for label-free or label-based proteomic experiments

Example dataset from a label-based SRM experiment of a time course yeast study

testResultMultiComparisons

Significance testing result of a set of comparisons between two groups

transformMSstatsToMSnSet

Transformation input format for MSstats to MSnSet class

Data pre-processing and quality control of MS runs of raw data

dataProcessPlots

Visualization for explanatory data analysis