# Analytical R tools for Mass Spectrometry

## Documentation for package ‘artMS’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

artmsAnalysisQuantifications | Analysis of the Relative Quantifications
artmsAnnotateSpecie | Adding a column with the species name
artmsAnnotationUniprot | Annotate table with Gene Symbol and Name based on Uniprot ID(s)
artmsAvgIntensityRT | Summarize average intensity and retention time per protein
artmsChangeColumnName | Change a specific column name in a given data.frame
artmsConvertMetabolomics | Convert Markview Metabolomics file (alignment table) into a artMS compatible format
artmsDataPlots | Individual Normalized abundance dot plots for every protein
artmsEnrichLog2fc | Enrichment of changes in protein abundance or PTMs
artmsEnrichProfiler | Enrichment analysis using GprofileR
artmsEvidenceToSaintExpress | MaxQuant evidence file to SAINTexpress format
artmsEvidenceToSAINTq | MaxQuant evidence file to SAINTq format
artmsFilterEvidenceContaminants | Remove contaminants and empty proteins from the MaxQuant evidence file
artmsGeneratePhSiteExtended | Generate ph-site specific detailed file
artmsIsEvidenceNewVersion | Check if a given evidencee file was generated by a new version of MaxQuant (v>1)
artmsIsSpeciesSupported | Check if a species is supported and available
artmsLeaveOnlyUniprotEntryID | Leave only the Entry ID from a typical full Uniprot IDs in a given column
artmsMapUniprot2Entrez | Map GENE SYMBOL, NAME, AND ENTREZID to a vector of Uniprot IDS
artmsMergeEvidenceAndKeys | Merge evidence.txt (or summary.txt) with keys.txt files
artmsMsstatsSummary | Summarize the MSStats results and data quantification
artmsPhosfateOutput | Generate Phosfate Input file
artmsPhotonOutput | Generate PHOTON Input file
artmsPlotHeatmapQuant | Outputs a heatmap of the MSStats results created using the log2fold changes
artmsProtein2SiteConversion | Converts the Protein ID column of the evidence file selected by the user to mod-site-specific notation: 'ProteinID' to 'ProteinID_AAnumber' notation
artmsQualityControlEvidenceBasic | Quality Control analysis of the MaxQuant evidence file
artmsQualityControlEvidenceExtended | Extended Quality Control of the MaxQuant evidence.txt file
artmsQualityControlMetabolomics | Quality Control analysis of the evidence-like metabolomics dataset
artmsQualityControlSummaryExtended | Quality Control of the MaxQuant summary.txt file
artmsQuantification | Relative quantification using MSstats
artmsResultsWide | Reshape the MSstats results file from long to wide format
artmsSILACtoLong | Convert the SILAC evidence file to MSstats format
artmsSpectralCounts | Outputs the spectral counts from the MaxQuant evidence file.
artmsVolcanoPlot | Volcano plot (log2fc / pvalues)
artmsWriteConfigYamlFile | Write out a template file of the artMS configuration file (yaml)
artms_config | artMS configuration template
artms_data_corum_mito_database | CORUM Protein Complexes database use for complex enrichment analysis
artms_data_pathogen_LPN | LPN PATHOGEN: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) UNIPROT IDS
artms_data_pathogen_TB | TB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) UNIPROTS IDS
artms_data_ph_config | artMS configuration for the available PH dataset
artms_data_ph_contrast | Contrast example for the PH dataset
artms_data_ph_evidence | Evidence file example
artms_data_ph_keys | Keys File Example
artms_data_ph_msstats_modelqc | MSstats modelQC example
artms_data_ph_msstats_results | MSstats results example
artms_data_randomDF | Random data set