Extract information from a pdAnalysis file

Read a .pdAnalysis file from Proteome Discoverer and extract information about the run.

getContaminantsDatabaseFrompdAnalysis(pdAnalysisFile)

getSearchParametersFrompdAnalysis(pdAnalysisFile)

getMaxMissedCleavagesFrompdAnalysis(pdAnalysisFile)

getQuantOrderFrompdAnalysis(pdAnalysisFile)

getTemplateNamesFrompdAnalysis(pdAnalysisFile)

getValidationInfoFrompdAnalysis(pdAnalysisFile)

getPSMValidationInfoFrompdAnalysis(pdAnalysisFile)

getCalibrationFrompdAnalysis(pdAnalysisFile)

getQuantInfoFrompdAnalysis(pdAnalysisFile)

Arguments

pdAnalysisFile

Path to a .pdAnalysis file from Proteome Discoverer.

Value

The extracted information from the .pdAnalysis file.

Author

Charlotte Soneson

Examples

getContaminantsDatabaseFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> $contaminantDb
#> [1] "CON_iRT_contaminants_cRAPMaxQFMI_150507.fasta"
#> 
#> $protMarkers
#> [1] "Contaminants"        "YEAST"               "YEAST__210503.fasta"
#> 

getSearchParametersFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> $search_engine
#> [1] "Sequest HT"
#> 
#> $fasta_db
#> [1] "CON_iRT_contaminants_cRAPMaxQFMI_150507.fasta; YEAST__210503.fasta"
#> 
#> $enzymes
#> [1] "Trypsin (Full)"
#> 
#> $dynamicModifications
#> [1] "Oxidation / +15.995 Da (M)"        "Carbamidomethyl / +57.021 Da (C)" 
#> [3] "TMTpro / +304.207 Da (K, S, T)"    "TMTpro / +304.207 Da (N-Terminus)"
#> 
#> $staticModifications
#> character(0)
#> 

getMaxMissedCleavagesFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> [1] "2"

getQuantOrderFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> [1] "MS3"

getTemplateNamesFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> $Consensus
#> [1] "CWF_Comprehensive_Enhanced Annotation_Reporter_Quan"
#> 
#> $Processing
#> [1] "PWF_Tribrid_TMTpro_Quan_SPS_MS3_SequestHT_Percolator"
#> 

getValidationInfoFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> $targetFDRstrictPSM
#> [1] "0.01"
#> 
#> $targetFDRrelaxedPSM
#> [1] "0.05"
#> 
#> $targetFDRstrictPeptide
#> [1] "0.01"
#> 
#> $targetFDRrelaxedPeptide
#> [1] "0.05"
#> 
#> $validationMethod
#> [1] "PercolatorConfidenceAssignment"
#> 
#> $validationBasedOn
#> [1] "Target/Decoy, q-Value"
#> 

getPSMValidationInfoFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> [1] "Percolator"

getCalibrationFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> [1] FALSE

getQuantInfoFrompdAnalysis(
    system.file("extdata", "pdtmt_example",
                "Fig2_m23139_RTS_QC_varMods.pdAnalysis",
                package = "einprot"))
#> $quant_mode
#> [1] "Reporter Ions Quantifier"
#> 
#> $peptides_to_use
#> [1] "Unique + Razor"
#> 
#> $abundance_based_on
#> [1] "S/N"
#> 
#> $quan_value_corr
#> [1] "False"
#> 
#> $co_isolation_thr
#> [1] "50"
#> 
#> $ave_reporter_sn_thr
#> [1] "10"
#> 
#> $sps_mm_pct_thr
#> [1] "65"
#> 
#> $norm_mode
#> [1] "Total Peptide Amount"
#> 
#> $imputation_mode
#> [1] "None"
#>