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docs(fragpipe): Modify vignettes to include global profiling run example (#119)
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-13
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+132
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‎DESCRIPTION‎

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Original file line numberDiff line numberDiff line change
@@ -40,5 +40,5 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, DifferentialE
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BugReports: https://github.com/Vitek-Lab/MSstatsPTM/issues
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3
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Config/testthat/edition: 3

‎R/converters.R‎

Lines changed: 13 additions & 5 deletions
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@@ -241,25 +241,33 @@ DIANNtoMSstatsPTMFormat = function(input,
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#' head(msstats_data$PTM)
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#' head(msstats_data$PROTEIN)
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#'
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#' # LFQ Example (w/out global profiling run)
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#' # LFQ Example
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#' input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv",
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#' package = "MSstatsPTM")
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#' input = data.table::fread(input)
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#' annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv",
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#' package = "MSstatsPTM")
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#' annot = data.table::fread(annot)
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#' annot = data.table::fread(annot)
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#' input_protein = system.file("tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv",
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#' package = "MSstatsPTM")
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#' input_protein = data.table::fread(input_protein)
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#'
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#' msstats_data = FragPipetoMSstatsPTMFormat(input,
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#' annot,
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#' input_protein = input_protein,
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#' label_type="LF",
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#' mod_id_col = "STY",
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#' localization_cutoff=.75,
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#' protein_id_col = "ProteinName",
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#' peptide_id_col = "PeptideSequence")
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#' head(msstats_data$PTM)
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#'
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#' # If no global profiling run is available, omit input_protein and set:
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#' # msstats_data = FragPipetoMSstatsPTMFormat(input, annot,
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#' # label_type = "LF", mod_id_col = "STY",
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#' # localization_cutoff = .75, protein_id_col = "ProteinName",
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#' # peptide_id_col = "PeptideSequence", use_unmod_peptides = FALSE)
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#'
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#' # Note that this is NULL because we did not include a global profiling run.
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#' # Ideally, you should include an independent global profiling run.
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#' head(msstats_data$PTM)
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#' head(msstats_data$PROTEIN)
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#'
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FragPipetoMSstatsPTMFormat = function(input,

‎inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,97 @@
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ProteinName,PeptideSequence,PrecursorCharge,FragmentIon,ProductCharge,IsotopeLabelType,Condition,BioReplicate,Run,Intensity
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sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
3+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
4+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA
6+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,44400.42
7+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA
8+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
9+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
10+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
11+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
12+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
13+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA
14+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,54096.2
15+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA
16+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,42032.559
17+
sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
18+
sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
19+
sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,45441.47
20+
sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
23+
sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
26+
sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
27+
sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,39071.486
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,49027.117
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,25728.36
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,50606.861
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
35+
sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,29068.013
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,48775.5
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
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sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,2,CR_Tio2-WT_1715,35259.795
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
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sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
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sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
51+
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,47090.12
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sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA
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sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
55+
sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA
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sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
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sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
59+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
60+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,182842.8
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,91160.492
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,121482.805
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,50779.54
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
66+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
67+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
68+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
69+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,55273.465
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,27288.379
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,56355.08
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,23782.973
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
75+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,30869.537
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,30077.96
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
81+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
84+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,19424.299
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,18153.773
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
89+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
90+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
91+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
93+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,50823.02
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,83515.89
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sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
97+
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA

‎man/FragPipetoMSstatsPTMFormat.Rd‎

Lines changed: 13 additions & 5 deletions
Some generated files are not rendered by default. Learn more about customizing how changed files appear on GitHub.

‎vignettes/MSstatsPTM_LabelFree_Workflow.Rmd‎

Lines changed: 8 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -140,22 +140,28 @@ msstats_data = FragPipetoMSstatsPTMFormat(fragpipe_input,
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head(msstats_data$PTM)
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head(msstats_data$PROTEIN)
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# LFQ Example (w/out global profiling run)
143+
# LFQ Example
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input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv",
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package = "MSstatsPTM")
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input = data.table::fread(input)
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annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv",
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package = "MSstatsPTM")
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annot = data.table::fread(annot)
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annot = data.table::fread(annot)
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input_protein = system.file("tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv",
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package = "MSstatsPTM")
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input_protein = data.table::fread(input_protein) # Global profiling run
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msstats_data = FragPipetoMSstatsPTMFormat(input,
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annot,
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input_protein = input_protein,
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label_type="LF",
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mod_id_col = "STY",
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localization_cutoff=.75,
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protein_id_col = "ProteinName",
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peptide_id_col = "PeptideSequence")
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head(msstats_data$PTM)
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head(msstats_data$PROTEIN)
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```
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161167

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