Package: MSstatsLiP 1.19.0

Anthony Wu

MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

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

MSstatsLiP_1.19.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MSstatsLiP/json (API)

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

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

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

On BioConductor:MSstatsLiP-1.19.0(bioc 3.24)MSstatsLiP-1.18.0(bioc 3.23)

immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolcpp

6.15 score 7 stars 5 scripts 18 exports 197 dependencies

Last updated from:28c13fd171. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING221
linux-devel-arm64NOTE329
linux-devel-x86_64NOTE282
source / vignettesOK303
linux-release-arm64NOTE344
linux-release-x86_64NOTE421
macos-release-arm64NOTE177
macos-release-x86_64NOTE528
macos-oldrel-arm64NOTE183
macos-oldrel-x86_64NOTE356
windows-develNOTE291
windows-releaseNOTE342
windows-oldrelNOTE349
wasm-releaseOK212

Exports:annotSitecalculateProteolyticResistancecalculateTrypticitycorrelationPlotLiPdataProcessPlotsLiPdataSummarizationLiPDIANNtoMSstatsLiPFormatgroupComparisonLiPgroupComparisonPlotsLiPlocateModlocatePTMPCAPlotLiPResistanceBarcodePlotLiPSkylinetoMSstatsLiPFormatSpectronauttoMSstatsLiPFormatStructuralBarcodePlotLiPtidyFastatrypticHistogramLiP

Dependencies:abindaskpassbackportsbase64encBiocGenericsBiostringsbitbit64bitopsblobbootbroombslibcachemcallrcarcarDatacaToolscellrangercheckmateclicliprclustercolorspacecommonmarkconflictedcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdendextendDerivdigestdoBydplyrDTdtplyrellipseemmeansestimabilityevaluatefactoextraFactoMineRfarverfastmapflashClustfontawesomeforcatsforecastFormulafracdifffsgarglegenericsggplot2ggpubrggrepelggsciggsignifggtextgluegoogledrivegooglesheets4gplotsgridExtragridtextgtablegtoolshavenhighrhmshtmltoolshtmlwidgetshttridsIRangesirlbaisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleapslifecyclelimmalitedownlme4lmerTestlmtestlog4rlubridatemagrittrmarkdownmarrayMASSMatrixMatrixModelsmemoisemgcvmimeminqamodelrMSstatsMSstatsConvertMSstatsPTMMSstatsTMTmultcompViewmvtnormnlmenloptrnnetnumDerivopensslotelpbkrtestpillarpkgconfigplotlypngpolynompreprocessCoreprettyunitsprocessxprogresspromisespspurrrquantregR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchrematch2reprexrlangrmarkdownrstatixrstudioapirvestS4VectorsS7sassscalesscatterplot3dselectrSeqinfoshowtextshowtextdbSparseMstatmodstringistringrsurvivalsyssysfontssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetimeDatetinytextzdburcautf8uuidvctrsviridisviridisLitevroomwithrxfunxml2XVectoryamlzoo

Proteolytic resistance analysis
MSstatsLiP Workflow: Protease resistance analysis | 1. Installation | 2. Data preprocessing | 2.1 Load datasets | 2.2 Select only fully tryptic (FT) peptides in both LiP and TrP dataset | 2.3 Correct nomenclature | Step 1: | Step 2: | 2.4 Data Summarization | 3. Modelling | 4. Calculate proteolytic resistance ratios | 5. Proteolytic resistance differential analysis | 6. Save outputs | 7. Plot aSynuclein proteolytic resistance DA result as barcode
Rendered fromProteolytic_resistance_notebook.Rmdusingknitr::rmarkdown

Last update: 2022-09-27
Started: 2022-04-18

MSstatsLiP Workflow: An example workflow and analysis of the MSstatsLiP package
MSstatsLiP Workflow Vignette | Installation | Workflow | 1. Preprocessing | 1.1 Raw Data Format | 1.2 Converter | 2. Summarization | 2.1 Summarization Function | 2.2 Tryptic barplot | 2.3 Run Correlation Plot | 2.4 Coefficient of Variation | 2.5 QCPlot | 2.6 Profile Plot | 2.7 PCA Plot | 2.8 Calculate Trypticity | 3. Modeling | 3.1 Function | 3.2 Volcano Plot | 3.3 Heatmap | 3.4 Barcode | 3.5 Calculate proteolytic resistance ratios
Rendered fromMSstatsLiP_Workflow.Rmdusingknitr::rmarkdown

Last update: 2022-09-27
Started: 2021-03-11

Readme and manuals

Help Manual

Help pageTopics
Annotate modification siteannotSite
Calcutates proteolytic resistance for provided data. Requires input from dataSummarizationLiP function. Can optionally calculate differential analysis using proteolytic resistance. In order for this function to work, Conditions and run numbers must match between the LiP and TrP data.calculateProteolyticResistance
Calculates level of trypticity for a list of LiP Peptides.calculateTrypticity
Plot run correlation for provided LiP and TrP experiment.correlationPlotLiP
Visualization for explanatory data analysisdataProcessPlotsLiP
Summarizes LiP and TrP datasets seperately using methods from MSstats.dataSummarizationLiP
Converts raw LiP MS data from DIA-NN into the format needed for MSstatsLiP.DIANNtoMSstatsLiPFormat
Model LiP and TrP data and make adjustments if needed Returns list of three modeled datasetsgroupComparisonLiP
Visualization for model-based analysis and summarizationgroupComparisonPlotsLiP
LiPRawDataLiPRawData
Locate modified sites with a peptidelocateMod
Annotate modified sites with associated peptideslocatePTM
MSstatsLiP_dataMSstatsLiP_data
MSstatsLiP_modelMSstatsLiP_model
MSstatsLiP_SummarizedMSstatsLiP_Summarized
Visualize PCA analysis for LiP and TrP datasets.PCAPlotLiP
raw_lipraw_lip
raw_protraw_prot
Proteolytic Resistance Barcode plot. Shows accessibility score of different fully tryptic peptides in a protein.ResistanceBarcodePlotLiP
SkylineTestSkylineTest
Converts raw LiP MS data from Skyline into the format needed for MSstatsLiP.SkylinetoMSstatsLiPFormat
Converts raw LiP MS data from Spectronaut into the format needed for MSstatsLiP.SpectronauttoMSstatsLiPFormat
Barcode plot. Shows protein coverge of LiP modified peptides.StructuralBarcodePlotLiP
Read and tidy a FASTA filetidyFasta
TrPRawDataTrPRawData
Histogram of Half vs Fully tryptic peptides. Calculates proteotypicity, and then uses calcualtions in histogram.trypticHistogramLiP