Package: MSstats 4.15.0

Meena Choi

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

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

Authors:Meena Choi [aut, cre], Mateusz Staniak [aut], Tsung-Heng Tsai [aut], Ting Huang [aut], Olga Vitek [aut]

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MSstats.pdf |MSstats.html✨
MSstats/json (API)

# Install 'MSstats' in R:

install.packages('MSstats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

DDARawData - Example dataset from a label-free DDA, a controlled spike-in experiment.
DDARawData.Skyline - Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.
DIARawData - Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.
SRMRawData - Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study
example_SDRF - Example SDRF.

On BioConductor:MSstats-4.13.4(bioc 3.20)MSstats-4.12.1(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology massspectrometry proteomics software normalization qualitycontrol timecourse

8.19 score 6 packages 142 scripts 806 downloads 115 mentions 45 exports 91 dependencies

Last updated 19 days agofrom:e7b07e5e42. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win-x86_64	WARNING	Oct 30 2024
R-4.5-linux-x86_64	WARNING	Oct 30 2024
R-4.4-win-x86_64	WARNING	Oct 30 2024
R-4.4-mac-x86_64	WARNING	Oct 30 2024
R-4.4-mac-aarch64	WARNING	Oct 30 2024
R-4.3-win-x86_64	WARNING	Oct 30 2024
R-4.3-mac-x86_64	WARNING	Oct 30 2024
R-4.3-mac-aarch64	WARNING	Oct 30 2024

Exports:checkRepeatedDesign dataProcess dataProcessPlots designSampleSize designSampleSizePlots DIANNtoMSstatsFormat DIAUmpiretoMSstatsFormat extractSDRF FragPipetoMSstatsFormat getProcessed getSamplesInfo getSelectedProteins groupComparison groupComparisonPlots groupComparisonQCPlots makePeptidesDictionary MaxQtoMSstatsFormat modelBasedQCPlots MSstatsContrastMatrix MSstatsGroupComparison MSstatsGroupComparisonOutput MSstatsGroupComparisonSingleProtein MSstatsHandleMissing MSstatsMergeFractions MSstatsNormalize MSstatsPrepareForDataProcess MSstatsPrepareForGroupComparison MSstatsPrepareForSummarization MSstatsSelectFeatures MSstatsSummarizationOutput MSstatsSummarize MSstatsSummarizeSingleLinear MSstatsSummarizeSingleTMP MSstatsSummarizeWithSingleCore OpenMStoMSstatsFormat OpenSWATHtoMSstatsFormat PDtoMSstatsFormat ProgenesistoMSstatsFormat quantification savePlot SDRFtoAnnotation SkylinetoMSstatsFormat SpectronauttoMSstatsFormat theme_msstats validateAnnotation

Dependencies:askpass backports base64enc bitops boot bslib cachem caTools checkmate cli colorspace cpp11 crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome fs generics ggplot2 ggrepel glue gplots gtable gtools highr htmltools htmlwidgets httr isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle limma lme4 log4r magrittr marray MASS Matrix memoise mgcv mime minqa MSstatsConvert munsell nlme nloptr openssl pillar pkgconfig plotly preprocessCore promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen rlang rmarkdown sass scales statmod stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

MSstats: End to End Workflow

Rendered fromMSstatsWorkflow.Rmdusingknitr::knitron Oct 30 2024.

Last update: 2024-10-15
Started: 2024-10-15

MSstats: Protein/Peptide significance analysis

Rendered fromMSstats.Rmdusingknitr::knitron Oct 30 2024.

Last update: 2023-07-28
Started: 2015-10-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if data represents repeated measurements design	checkRepeatedDesign
Process MS data: clean, normalize and summarize before differential analysis	dataProcess
Visualization for explanatory data analysis	dataProcessPlots
Example dataset from a label-free DDA, a controlled spike-in experiment.	DDARawData
Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.	DDARawData.Skyline
Planning future experimental designs of Selected Reaction Monitoring (SRM), Data-Dependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA or SWATH-MS) experiments in sample size calculation	designSampleSize
Visualization for sample size calculation	designSampleSizePlots
Import Diann files	DIANNtoMSstatsFormat
Example dataset from a label-free DIA, a group comparison study of S.Pyogenes.	DIARawData
Import DIA-Umpire files	DIAUmpiretoMSstatsFormat
Example SDRF.	example_SDRF
Extract experimental design from MSstats format into SDRF format	extractSDRF
Import FragPipe files	FragPipetoMSstatsFormat
Get feature-level data to be used in the MSstatsSummarizationOutput function	getProcessed
Get information about number of measurements for each group	getSamplesInfo
Get proteins based on names or integer IDs	getSelectedProteins
Whole plot testing	groupComparison
Visualization for model-based analysis and summarizing differentially abundant proteins	groupComparisonPlots
Visualization for model-based quality control in fitting model	groupComparisonQCPlots
Prepare a peptides dictionary for global standards normalization	makePeptidesDictionary
Import MaxQuant files	MaxQtoMSstatsFormat
Visualization for model-based quality control in fitting model	modelBasedQCPlots
Create a contrast matrix for groupComparison function	MSstatsContrastMatrix
Group comparison	MSstatsGroupComparison
Create output of group comparison based on results for individual proteins	MSstatsGroupComparisonOutput
Group comparison for a single protein	MSstatsGroupComparisonSingleProtein
Handle censored missing values	MSstatsHandleMissing
Re-format the data before feature selection	MSstatsMergeFractions
Normalize MS data	MSstatsNormalize
Prepare data for processing by `dataProcess` function	MSstatsPrepareForDataProcess
Prepare output for dataProcess for group comparison	MSstatsPrepareForGroupComparison
Prepare feature-level data for protein-level summarization	MSstatsPrepareForSummarization
Feature selection before feature-level data summarization	MSstatsSelectFeatures
Post-processing output from MSstats summarization	MSstatsSummarizationOutput
Feature-level data summarization	MSstatsSummarize
Linear model-based summarization for a single protein	MSstatsSummarizeSingleLinear
Tukey Median Polish summarization for a single protein	MSstatsSummarizeSingleTMP
Feature-level data summarization with multiple cores	MSstatsSummarizeWithMultipleCores
Feature-level data summarization with 1 core	MSstatsSummarizeWithSingleCore
Import OpenMS files	OpenMStoMSstatsFormat
Import OpenSWATH files	OpenSWATHtoMSstatsFormat
Import Proteome Discoverer files	PDtoMSstatsFormat
Import Progenesis files	ProgenesistoMSstatsFormat
Protein sample quantification or group quantification	quantification
Save a plot to pdf file	savePlot
Convert SDRF experimental design file into an MSstats annotation file	SDRFtoAnnotation
Import Skyline files	SkylinetoMSstatsFormat
Import Spectronaut files	SpectronauttoMSstatsFormat
Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study	SRMRawData
Theme for MSstats plots	theme_msstats
Check if annotation matches intended experimental design	validateAnnotation