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docs(fragpipe): Update vignettes and documentation for Fragpipe conve…
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…rter (#90)
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tonywu1999 authored Jun 1, 2024
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28 changes: 26 additions & 2 deletions R/converters.R
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,9 @@ DIANNtoMSstatsPTMFormat = function(input,
#' @param mod_id_col Column containing the modified Amino Acids. For example, a Phosphorylation experiment may pass `STY`. The corresponding column with `STY` combined with the mass (e.x. `STY.79.9663`) will be selected. Default is `STY`.
#' @param localization_cutoff Minimum localization score required to keep modification. Default is .75.
#' @param remove_unlocalized_peptides Boolean indicating if peptides without all sites localized should be kept. Default is TRUE (non-localized sites will be removed).
#' @param Purity_cutoff Cutoff for purity. Default is 0.6
#' @param Purity_cutoff Cutoff for purity. Default is 0.6. Purity refers to how much of the detected ion signal
#' within a specific inclusion window belongs to the target molecule or its closely related forms,
#' compared to any other unwanted signals or noise. Higher values indicate greater purity.
#' @param PeptideProphet_prob_cutoff Cutoff for the peptide identification probability. Default is 0.7.
#' The probability is confidence score determined by PeptideProphet and higher values indicate greater confidence.
#' @param useUniquePeptide logical, if TRUE (default) removes peptides that are assigned for more than one proteins.
Expand All @@ -209,7 +211,7 @@ DIANNtoMSstatsPTMFormat = function(input,
#' @export
#'
#' @examples
#' # TMT Example
#' # TMT Example (with global profiling run)
#' head(fragpipe_input)
#' head(fragpipe_annotation)
#' head(fragpipe_input_protein)
Expand All @@ -225,6 +227,28 @@ DIANNtoMSstatsPTMFormat = function(input,
#' remove_unlocalized_peptides=TRUE)
#' head(msstats_data$PTM)
#' head(msstats_data$PROTEIN)
#'
#' # LFQ Example (w/out global profiling run)
#' input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv",
#' package = "MSstatsPTM")
#' input = data.table::fread(input)
#' annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv",
#' package = "MSstatsPTM")
#' annot = data.table::fread(annot)
#'
#' msstats_data = FragPipetoMSstatsPTMFormat(input,
#' annot,
#' label_type="LF",
#' mod_id_col = "STY",
#' localization_cutoff=.75,
#' protein_id_col = "ProteinName",
#' peptide_id_col = "PeptideSequence")
#' head(msstats_data$PTM)
#'
#' # Note that this is NULL because we did not include a global profiling run.
#' # Ideally, you should include an independent global profiling run.
#' head(msstats_data$PROTEIN)
#'
FragPipetoMSstatsPTMFormat = function(input,
annotation=NULL,
input_protein=NULL,
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97 changes: 97 additions & 0 deletions inst/tinytest/raw_data/Fragpipe/MSstats.csv
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@@ -0,0 +1,97 @@
ProteinName,PeptideSequence,Protein.Start,Protein.End,PrecursorCharge,FragmentIon,ProductCharge,IsotopeLabelType,Condition,BioReplicate,Run,Intensity,M:15.9949,STY:79.9663
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,34400.42,NA,MIGVLNNS(0.8834)S(0.0373)ES(0.0373)DEEES(0.0420)NDEKQK
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNS[79.9663]SESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,34096.2,NA,MIGVLNNS(0.0197)S(0.4789)ES(0.4789)DEEES(0.0224)NDEKQK
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA,NA,NA
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,22032.559,NA,MIGVLNNS(0.0179)S(0.4821)ES(0.4821)DEEES(0.0180)NDEKQK
sp|O13563|RPN13_YEAST,MIGVLNNSS[79.9663]ESDEEESNDEKQK,125,146,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,35441.47,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,19071.486,NA,MES(0.0145)QQLS(0.0162)QHS(0.9096)PIS(0.0150)HGS(0.0115)ACAS(0.0111)VT(0.0110)S(0.0110)K
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,46027.117,NA,MES(0.0117)QQLS(0.0134)QHS(0.9004)PIS(0.0121)HGS(0.0166)ACAS(0.0150)VT(0.0144)S(0.0164)K
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,35728.36,NA,MES(0.0117)QQLS(0.0191)QHS(0.9087)PIS(0.0134)HGS(0.0119)ACAS(0.0119)VT(0.0116)S(0.0116)K
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MESQQLSQHS[79.9663]PISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,10606.861,NA,MES(0.0084)QQLS(0.0101)QHS(0.9070)PIS(0.0249)HGS(0.0123)ACAS(0.0110)VT(0.0131)S(0.0131)K
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,9068.013,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,43775.5,NA,MES(0.3178)QQLS(0.3178)QHS(0.3178)PIS(0.0075)HGS(0.0072)ACAS(0.0097)VT(0.0096)S(0.0126)K
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|O74302|YD13A_YEAST,n[42.0106]MES[79.9663]QQLSQHSPISHGSAC[57.0215]ASVTSK,1,24,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,WT,2,CR_Tio2-WT_1715,25259.795,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,20,44,2,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,37090.12,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,81,97,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,112842.8,NA,FAT(0.0204)VPT(0.0207)GGAS(0.0211)S(0.0212)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9166)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,51160.492,NA,FAT(0.0157)VPT(0.0166)GGAS(0.0167)S(0.0168)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9343)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,128482.805,NA,FAT(0.0193)VPT(0.0198)GGAS(0.0213)S(0.0221)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9175)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,50779.54,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,45273.465,NA,FAT(0.0214)VPT(0.0216)GGAS(0.0218)S(0.0218)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9134)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,27288.379,NA,FAT(0.0162)VPT(0.0165)GGAS(0.0165)S(0.0158)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9350)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,56355.08,NA,FAT(0.0183)VPT(0.0182)GGAS(0.0182)S(0.0182)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9272)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,23782.973,NA,FAT(0.0179)VPT(0.0181)GGAS(0.0181)S(0.0181)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9278)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDMGFGLFD,63,110,4,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,30869.537,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDM(1.0000)GFGLFD,FAT(0.0241)VPT(0.0263)GGAS(0.0208)S(0.0210)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9078)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,30077.96,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDM(1.0000)GFGLFD,FAT(0.0342)VPT(0.0510)GGAS(0.0649)S(0.0311)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.8189)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,19424.299,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDM(1.0000)GFGLFD,FAT(0.0216)VPT(0.0207)GGAS(0.0207)S(0.0208)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9162)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,18153.773,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDM(1.0000)GFGLFD,FAT(0.0181)VPT(0.0181)GGAS(0.0181)S(0.0181)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.9275)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEES[79.9663]DDDM[15.9949]GFGLFD,63,110,4,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,50823.02,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,83515.89,NA,FAT(0.0115)VPT(0.0121)GGAS(0.3255)S(0.3255)AAAGAAGAAAGGDAAEEEKEEEAKEES(0.3255)DDDMGFGLFD
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA,NA,NA
sp|P02400|RLA4_YEAST,FATVPTGGAS[79.9663]SAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,63,110,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA,NA,NA
9 changes: 9 additions & 0 deletions inst/tinytest/raw_data/Fragpipe/experiment_annotation.tsv
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Original file line number Diff line number Diff line change
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file sample sample_name condition replicate
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\mutant\CR_Tio2-phos85D_1716.d MUT_1 MUT_1 MUT 1
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\mutant\JCI-TiO2-DDAphosMethod-rho_1339.d MUT_2 MUT_2 MUT 2
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\mutant\JCI-TiO2-DDAstd-rho_1336.d MUT_3 MUT_3 MUT 3
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\mutant\JCI_230921_TiO2-phos85D_1660.d MUT_4 MUT_4 MUT 4
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\WT\3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199.d WT_1 WT_1 WT 1
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\WT\CR_Tio2-WT_1715.d WT_2 WT_2 WT 2
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\WT\JCI-TiO2-DDAphosMethod-WT_1338.d WT_3 WT_3 WT 3
E:\Edmond\jennifer_PTM\ptm\LFQ_yeast_phospho_email\dda_phospho_raw\WT\JCI-TiO2-DDAstd-WT_1335.d WT_4 WT_4 WT 4
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