Package: MSstatsTMT 2.21.0

Devon Kohler

MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Authors:Devon Kohler [aut, cre], Ting Huang [aut], Meena Choi [aut], Mateusz Staniak [aut], Tony Wu [aut], Deril Raju [aut], Sicheng Hao [aut], Olga Vitek [aut]

MSstatsTMT_2.21.0.tar.gz
MSstatsTMT_2.21.0.zip(r-4.7)MSstatsTMT_2.21.0.zip(r-4.6)MSstatsTMT_2.21.0.zip(r-4.5)
MSstatsTMT_2.21.0.tgz(r-4.6-any)MSstatsTMT_2.21.0.tgz(r-4.5-any)
MSstatsTMT_2.21.0.tar.gz(r-4.7-any)MSstatsTMT_2.21.0.tar.gz(r-4.6-any)
MSstatsTMT_2.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MSstatsTMT/json (API)

# Install 'MSstatsTMT' in R:

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

Datasets:

annotation.mine - Example of annotation file for raw.mine, which is the output of SpectroMine.
annotation.mq - Example of annotation file for evidence, which is the output of MaxQuant.
annotation.pd - Example of annotation file for raw.pd, which is the PSM output of Proteome Discoverer
evidence - Example of output from MaxQuant for TMT-10plex experiments.
input.pd - Example of output from PDtoMSstatsTMTFormat function
proteinGroups - Example of proteinGroups file from MaxQuant for TMT-10plex experiments.
raw.mine - Example of output from SpectroMine for TMT-6plex experiments.
raw.om - Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.
raw.pd - Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.

On BioConductor:MSstatsTMT-2.21.0(bioc 3.24)MSstatsTMT-2.20.0(bioc 3.23)

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

immunooncology massspectrometry proteomics software

6.50 score 3 packages 71 scripts 708 downloads 5 mentions 9 exports 95 dependencies

Last updated from:1dff091661. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	178
linux-devel-x86_64	NOTE	266
source / vignettes	OK	201
linux-release-x86_64	NOTE	301
macos-release-arm64	NOTE	165
macos-oldrel-arm64	NOTE	143
windows-devel	NOTE	173
windows-release	NOTE	217
windows-oldrel	NOTE	211
wasm-release	OK	140

Exports:dataProcessPlotsTMT designSampleSizeTMT groupComparisonTMT MaxQtoMSstatsTMTFormat OpenMStoMSstatsTMTFormat PDtoMSstatsTMTFormat PhilosophertoMSstatsTMTFormat proteinSummarization SpectroMinetoMSstatsTMTFormat

Dependencies:askpass backports base64enc bitops boot bslib cachem caTools checkmate cli cpp11 crosstalk curl data.table digest dplyr evaluate 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 lmerTest log4r magrittr marray MASS Matrix memoise mime minqa MSstats MSstatsConvert nlme nloptr numDeriv openssl otel pillar pkgconfig plotly preprocessCore promises purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown S7 sass scales statmod stringi stringr survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

MSstatsTMT : A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Rendered fromMSstatsTMT.Rmdusingknitr::rmarkdown

Last update: 2022-02-18
Started: 2017-12-13

Help page	Topics
Example of annotation file for raw.mine, which is the output of SpectroMine.	annotation.mine
Example of annotation file for evidence, which is the output of MaxQuant.	annotation.mq
Example of annotation file for raw.pd, which is the PSM output of Proteome Discoverer	annotation.pd
Visualization for explanatory data analysis - TMT experiment	dataProcessPlotsTMT
Planning future experimental designs of Tandem Mass Tag (TMT) experiments acquired with Data-Dependent Acquisition (DDA or shotgun)	designSampleSizeTMT
Example of output from MaxQuant for TMT-10plex experiments.	evidence
Finding differentially abundant proteins across conditions in TMT experiment	groupComparisonTMT
Example of output from PDtoMSstatsTMTFormat function	input.pd
Generate MSstatsTMT required input format from MaxQuant output	MaxQtoMSstatsTMTFormat
MSstatsTMT: A package for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	MSstatsTMT-package MSstatsTMT
Generate MSstatsTMT required input format for OpenMS output	OpenMStoMSstatsTMTFormat
Convert Proteome Discoverer output to MSstatsTMT format.	PDtoMSstatsTMTFormat
Convert Philosopher (Fragpipe) output to MSstatsTMT format.	PhilosophertoMSstatsTMTFormat
Example of proteinGroups file from MaxQuant for TMT-10plex experiments.	proteinGroups
Summarizing peptide level quantification to protein level quantification	proteinSummarization
Example of output from SpectroMine for TMT-6plex experiments.	raw.mine
Example of MSstatsTMT report from OpenMS for TMT-10plex experiments.	raw.om
Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.	raw.pd
Import data from SpectroMine	SpectroMinetoMSstatsTMTFormat

Package: MSstatsTMT 2.21.0

MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Citation

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)