Package: MSstatsPTM 2.15.0

Anthony Wu

MSstatsPTM: Statistical Characterization of Post-translational Modifications

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

Authors:Devon Kohler [aut], Tsung-Heng Tsai [aut], Anthony Wu [aut, cre], Deril Raju [aut], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Olga Vitek [aut]

MSstatsPTM_2.15.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
MSstatsPTM/json (API)

# Install 'MSstatsPTM' in R:
install.packages('MSstatsPTM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vitek-lab/msstatsptm/issues

Pkgdown/docs site:https://vitek-lab.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:MSstatsPTM-2.15.0(bioc 3.24)MSstatsPTM-2.14.0(bioc 3.23)

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolpost-translational-modificationcpp

8.46 score 14 stars 2 packages 53 scripts 557 downloads 22 exports 104 dependencies

Last updated from:7d1f703546. Checks:12 WARNING, 2 OK. Indexed: yes.

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Exports:annotSitedataProcessPlotsPTMdataProcessPTMdataSummarizationPTMdataSummarizationPTM_TMTdesignSampleSizePTMDIANNtoMSstatsPTMFormatFragPipetoMSstatsPTMFormatgroupComparisonPlotsPTMgroupComparisonPTMlocateModlocatePTMMaxQtoMSstatsPTMFormatMetamorpheusToMSstatsPTMFormatMSstatsPTMSiteLocatorPDtoMSstatsPTMFormatProgenesistoMSstatsPTMFormatProteinProspectortoMSstatsPTMFormatPStoMSstatsPTMFormatSkylinetoMSstatsPTMFormatSpectronauttoMSstatsPTMFormattidyFasta

Dependencies:askpassbackportsbase64encBiocGenericsBiostringsbitopsbootbslibcachemcaToolscheckmateclicpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2ggrepelgluegplotsgridExtragtablegtoolshighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4lmerTestlog4rmagrittrmarrayMASSMatrixmemoisemimeminqaMSstatsMSstatsConvertMSstatsTMTnlmenloptrnumDerivopensslotelpillarpkgconfigplotlypreprocessCorepromisespurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS4VectorsS7sassscalesSeqinfostatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml

MSstatsPTM LabelFree Workflow

Devon Kohler ([email protected])

Rendered fromMSstatsPTM_LabelFree_Workflow.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2025-09-17
Started: 2021-05-12

MSstatsPTM TMT Workflow

Devon Kohler ([email protected])

Rendered fromMSstatsPTM_TMT_Workflow.Rmdusingknitr::rmarkdownon May 26 2026.

Last update: 2025-03-13
Started: 2021-05-12

Readme and manuals

Help Manual

Help pageTopics
Fix terminus location adjustments.fixTerminus
Annotate modification siteannotSite
Visualization for explanatory data analysisdataProcessPlotsPTM
Data processing and summarization of peptide-level quantification to PTM and protein level quantificationdataProcessPTM
Data summarization function for label-free MS experiments targeting PTMs.dataSummarizationPTM
Data summarization function for TMT labelled MS experiments targeting PTMs.dataSummarizationPTM_TMT
Planning future experimental designs of PTM experiments in sample size calculationdesignSampleSizePTM
Convert the output of DIA-NN PSM file into MSstatsPTM formatDIANNtoMSstatsPTMFormat
Example annotation file for a TMT FragPipe experiment.fragpipe_annotation
Example annotation file for a global profiling run TMT FragPipe experiment.fragpipe_annotation_protein
Output of FragPipe TMT PTM experimentfragpipe_input
Output of FragPipe TMT global profiling experimentfragpipe_input_protein
Convert output of TMT labeled Fragpipe data into MSstatsPTM format.FragPipetoMSstatsPTMFormat
Visualization for model-based analysis and summarizationgroupComparisonPlotsPTM
Perform differential analysis on MS-based proteomics experiments targeting PTMsgroupComparisonPTM
Locate modified sites with a peptidelocateMod
Annotate modified sites with associated peptideslocatePTM
Example annotation file for a label-free MaxQuant experiment.maxq_lf_annotation
Example MaxQuant evidence file from the output of a label free experimentmaxq_lf_evidence
Example annotation file for a TMT MaxQuant experiment.maxq_tmt_annotation
Example MaxQuant evidence file from the output of a TMT experimentmaxq_tmt_evidence
Convert output of label-free or TMT MaxQuant experiments into MSstatsPTM formatMaxQtoMSstatsPTMFormat
Import Metamorpheus files into PTM formatMetamorpheusToMSstatsPTMFormat
Locate modification site number and amino acidMSstatsPTMSiteLocator
Example annotation file for a label-free Proteome Discoverer experiment.pd_annotation
Example Proteome Discoverer evidence file from the output of a label free experimentpd_psm_input
Example output of Proteome Discoverer converterpd_testing_output
Convert Proteome Discoverer output into MSstatsPTM formatPDtoMSstatsPTMFormat
Converts non-TMT Progenesis output into the format needed for MSstatsPTMProgenesistoMSstatsPTMFormat
Generate MSstatsPTM required input format from Protein Prospector outputProteinProspectortoMSstatsPTMFormat
Convert Peaks Studio output into MSstatsPTM formatPStoMSstatsPTMFormat
Example of input PTM dataset for LabelFree/DDA/DIA experiments.raw.input
Example of input PTM dataset for TMT experiments.raw.input.tmt
Convert Skyline output into MSstatsPTM formatSkylinetoMSstatsPTMFormat
Example annotation file for a label-free Spectronaut experiment.spectronaut_annotation
Example Spectronaut evidence file from the output of a label free experimentspectronaut_input
Convert Spectronaut output into MSstatsPTM formatSpectronauttoMSstatsPTMFormat
Example of output from dataSummarizationPTM function for non-TMT datasummary.data
Example of output from dataSummarizationPTM_TMT function for TMT datasummary.data.tmt
Read and tidy a FASTA filetidyFasta