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MSstats (version 2.4.0)

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

2.4.0

License

Artistic-2.0

Maintainer

Meena Choi

Last Published

February 15th, 2017

Functions in MSstats (2.4.0)

modelBasedQCPlots

Visualization for model-based quality control in fitting model
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
MSstats-package

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

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

Protein sample quantification or group quantification
RawData

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
dataProcess

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

Visualization for explanatory data analysis
transformMSstatsToMSnSet

Transformation input format for MSstats to MSnSet class
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