From f3252cf2bf24a2a14fdb2fe8ef2523ade8271ade Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Wed, 18 Feb 2026 14:48:23 -0500
Subject: [PATCH 1/5] initial fixes for the DIANN 2.0 PTM converter

---
 R/converters.R                                |  34 ++++++++++++++----
 .../DIANN/annotation_diann_2.0_ptm.csv        |   9 +++++
 .../raw_data/DIANN/diann_2_ptm.parquet        | Bin 0 -> 51941 bytes
 man/DIANNtoMSstatsPTMFormat.Rd                |  34 +++++++++++++++---
 4 files changed, 67 insertions(+), 10 deletions(-)
 create mode 100644 inst/tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv
 create mode 100644 inst/tinytest/raw_data/DIANN/diann_2_ptm.parquet

diff --git a/R/converters.R b/R/converters.R
index 108cc41..9e1796f 100644
--- a/R/converters.R
+++ b/R/converters.R
@@ -7,10 +7,8 @@
 #' 
 #' @importFrom data.table as.data.table
 #' @importFrom MSstatsConvert DIANNtoMSstatsFormat
+#' @inheritParams MSstatsConvert::DIANNtoMSstatsFormat
 #' 
-#' @param input data.frame of `report.tsv` file produced by Philosopher
-#' @param annotation annotation with Run, Fraction, TechRepMixture, Mixture, Channel, 
-#' BioReplicate, Condition columns or a path to file. Refer to the example 'annotation' for the meaning of each column.
 #' @param input_protein same as `input` for global profiling run. Default is NULL.
 #' @param annotation_protein same as `annotation` for global profiling run. Default is NULL.
 #' @param fasta_path A string of path to a FASTA file, used to match PTM peptides.
@@ -31,7 +29,6 @@
 #' @param removeFewMeasurements TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
 #' @param removeOxidationMpeptides TRUE (default) will remove the peptides including oxidation (M) sequence.
 #' @param removeProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
-#' @param MBR If analaysis was done with match between runs or not. Default is TRUE.
 #' @param use_log_file logical. If TRUE, information about data processing will 
 #' be saved to a file.
 #' @param append logical. If TRUE, information about data processing will be 
@@ -68,6 +65,28 @@
 #' 
 #' head(msstatsptm_format$PTM)
 #' 
+#' # Example DIANN 2.0
+#' input = system.file("tinytest/raw_data/DIANN/diann_2_ptm.parquet", 
+#'                                         package = "MSstatsPTM")
+#' input = arrow::read_parquet(input)
+#' annot = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv", 
+#'                                         package = "MSstatsPTM")
+#' annot = data.table::fread(annot)
+#' fasta_path = system.file("extdata", "diann.fasta", 
+#'                        package="MSstatsPTM")
+#' 
+#' msstatsptm_format = DIANNtoMSstatsPTMFormat(
+#'     input, 
+#'     annot, 
+#'     protein_id_col = "Protein.Names", 
+#'     fasta_path = fasta_path, 
+#'     fasta_protein_name = "entry_name", 
+#'     use_log_file = FALSE,
+#'     quantificationColumn = "auto"
+#' )
+#' 
+#' head(msstatsptm_format$PTM)
+#' 
 DIANNtoMSstatsPTMFormat = function(input,
                                    annotation,
                                    input_protein=NULL,
@@ -84,6 +103,7 @@ DIANNtoMSstatsPTMFormat = function(input,
                                    removeOxidationMpeptides = TRUE,
                                    removeProtein_with1Feature = FALSE,
                                    MBR=TRUE,
+                                   quantificationColumn = "FragmentQuantCorrected",
                                    use_log_file = TRUE,
                                    append = FALSE,
                                    verbose = TRUE,
@@ -133,7 +153,8 @@ DIANNtoMSstatsPTMFormat = function(input,
                                    append,
                                    verbose,
                                    log_file_path,
-                                   MBR)
+                                   MBR,
+                                   quantificationColumn = quantificationColumn)
   
   msstats_format = list(PTM=ptm_input, PROTEIN=NULL)
   
@@ -154,7 +175,8 @@ DIANNtoMSstatsPTMFormat = function(input,
                                          append,
                                          verbose,
                                          log_file_path,
-                                         MBR)
+                                         MBR,
+                                         quantificationColumn = quantificationColumn)
     
     msstats_format = list(PTM=ptm_input, PROTEIN=protein_input)
     
diff --git a/inst/tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv b/inst/tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv
new file mode 100644
index 0000000..d876c3b
--- /dev/null
+++ b/inst/tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv
@@ -0,0 +1,9 @@
+Run,BioReplicate,Condition
+Run1,1,Control
+Run2,2,Control
+Run3,3,Control
+Run4,4,Control
+Run5,5,Treatment
+Run6,6,Treatment
+Run7,7,Treatment
+Run8,8,Treatment
diff --git a/inst/tinytest/raw_data/DIANN/diann_2_ptm.parquet b/inst/tinytest/raw_data/DIANN/diann_2_ptm.parquet
new file mode 100644
index 0000000000000000000000000000000000000000..b3b64b0d0cc46a3f2c5682510fb4d0909c760b59
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diff --git a/man/DIANNtoMSstatsPTMFormat.Rd b/man/DIANNtoMSstatsPTMFormat.Rd
index b7a5c79..4c130a6 100644
--- a/man/DIANNtoMSstatsPTMFormat.Rd
+++ b/man/DIANNtoMSstatsPTMFormat.Rd
@@ -21,6 +21,7 @@ DIANNtoMSstatsPTMFormat(
   removeOxidationMpeptides = TRUE,
   removeProtein_with1Feature = FALSE,
   MBR = TRUE,
+  quantificationColumn = "FragmentQuantCorrected",
   use_log_file = TRUE,
   append = FALSE,
   verbose = TRUE,
@@ -28,10 +29,10 @@ DIANNtoMSstatsPTMFormat(
 )
 }
 \arguments{
-\item{input}{data.frame of \code{report.tsv} file produced by Philosopher}
+\item{input}{name of MSstats input report from Diann, which includes fragment-level data.
+Output fragment data with --export-quant flag in DIA-NN 2.0}
 
-\item{annotation}{annotation with Run, Fraction, TechRepMixture, Mixture, Channel,
-BioReplicate, Condition columns or a path to file. Refer to the example 'annotation' for the meaning of each column.}
+\item{annotation}{name of 'annotation.txt' data which includes Condition, BioReplicate, Run.}
 
 \item{input_protein}{same as \code{input} for global profiling run. Default is NULL.}
 
@@ -66,7 +67,11 @@ We assume to use unique peptide for each protein.}
 
 \item{removeProtein_with1Feature}{TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.}
 
-\item{MBR}{If analaysis was done with match between runs or not. Default is TRUE.}
+\item{MBR}{True if analysis was done with match between runs}
+
+\item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x.
+Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x.
+Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 
 \item{use_log_file}{logical. If TRUE, information about data processing will
 be saved to a file.}
@@ -112,4 +117,25 @@ msstatsptm_format = DIANNtoMSstatsPTMFormat(
 
 head(msstatsptm_format$PTM)
 
+# Example DIANN 2.0
+input = system.file("tinytest/raw_data/DIANN/diann_2_ptm.parquet", 
+                                        package = "MSstatsPTM")
+input = data.table::fread(input)
+annot = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv", 
+                                        package = "MSstatsPTM")
+annot = data.table::fread(annot)
+fasta_path = system.file("extdata", "diann.fasta", 
+                       package="MSstatsPTM")
+
+msstatsptm_format = DIANNtoMSstatsPTMFormat(
+    input, 
+    annot, 
+    protein_id_col = "Protein.Names", 
+    fasta_path = fasta_path, 
+    fasta_protein_name = "entry_name", 
+    use_log_file = FALSE
+)
+
+head(msstatsptm_format$PTM)
+
 }

From a8abaadd90ca0d4fa3988904b519de8049312cb7 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Wed, 18 Feb 2026 16:51:18 -0500
Subject: [PATCH 2/5] inheritParams of original converter

---
 R/converters.R                 | 74 +++++++++++++---------------------
 man/DIANNtoMSstatsPTMFormat.Rd | 46 ++++++++++++---------
 2 files changed, 55 insertions(+), 65 deletions(-)

diff --git a/R/converters.R b/R/converters.R
index 9e1796f..294d03e 100644
--- a/R/converters.R
+++ b/R/converters.R
@@ -20,24 +20,6 @@
 #' in `protein_id_col`. The protein names in these two columns must match in 
 #' order to join the FASTA file with the DIA-NN output. Default is "uniprot_ac"
 #' for uniprot ID. For uniprot mnemonic ID, use "entry_name"
-#' @param global_qvalue_cutoff The global qvalue cutoff. Default is 0.01.
-#' @param qvalue_cutoff local qvalue cutoff for library. Default is 0.01.
-#' @param pg_qvalue_cutoff local qvalue cutoff for protein groups Run should be 
-#' the same as filename. Default is 0.01.
-#' @param useUniquePeptide logical, if TRUE (default) removes peptides that are assigned for more than one proteins. 
-#' We assume to use unique peptide for each protein.
-#' @param removeFewMeasurements TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
-#' @param removeOxidationMpeptides TRUE (default) will remove the peptides including oxidation (M) sequence.
-#' @param removeProtein_with1Feature TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
-#' @param use_log_file logical. If TRUE, information about data processing will 
-#' be saved to a file.
-#' @param append logical. If TRUE, information about data processing will be 
-#' added to an existing log file.
-#' @param verbose logical. If TRUE, information about data processing wil be 
-#' printed to the console.
-#' @param log_file_path character. Path to a file to which information about 
-#' data processing will be saved. If not provided, such a file will be created 
-#' automatically. If 'append = TRUE', has to be a valid path to a file.
 #' 
 #' @return `list` of one or two `data.frame` of class `MSstatsTMT`, named `PTM` and `PROTEIN`
 #' 
@@ -140,20 +122,20 @@ DIANNtoMSstatsPTMFormat = function(input,
     input = input[input[,..protein_id_col][[1]] != input$ProteinNameUnmod]
   }
   
-  ptm_input = DIANNtoMSstatsFormat(input, 
-                                   annotation,
-                                   global_qvalue_cutoff,
-                                   qvalue_cutoff,
-                                   pg_qvalue_cutoff,
-                                   useUniquePeptide,
-                                   removeFewMeasurements,
-                                   removeOxidationMpeptides,
-                                   removeProtein_with1Feature,
-                                   use_log_file,
-                                   append,
-                                   verbose,
-                                   log_file_path,
-                                   MBR,
+  ptm_input = DIANNtoMSstatsFormat(input = input, 
+                                   annotation = annotation,
+                                   global_qvalue_cutoff = global_qvalue_cutoff,
+                                   qvalue_cutoff = qvalue_cutoff,
+                                   pg_qvalue_cutoff = pg_qvalue_cutoff,
+                                   useUniquePeptide = useUniquePeptide,
+                                   removeFewMeasurements = removeFewMeasurements,
+                                   removeOxidationMpeptides = removeOxidationMpeptides,
+                                   removeProtein_with1Feature = removeProtein_with1Feature,
+                                   use_log_file = use_log_file,
+                                   append = append,
+                                   verbose = verbose,
+                                   log_file_path = log_file_path,
+                                   MBR = MBR,
                                    quantificationColumn = quantificationColumn)
   
   msstats_format = list(PTM=ptm_input, PROTEIN=NULL)
@@ -162,20 +144,20 @@ DIANNtoMSstatsPTMFormat = function(input,
     checkmate::assertTRUE(!is.null(input_protein) & 
                             !is.null(annotation_protein))
     
-    protein_input = DIANNtoMSstatsFormat(input_protein, 
-                                         annotation_protein,
-                                         global_qvalue_cutoff,
-                                         qvalue_cutoff,
-                                         pg_qvalue_cutoff,
-                                         useUniquePeptide,
-                                         removeFewMeasurements,
-                                         removeOxidationMpeptides,
-                                         removeProtein_with1Feature,
-                                         use_log_file,
-                                         append,
-                                         verbose,
-                                         log_file_path,
-                                         MBR,
+    protein_input = DIANNtoMSstatsFormat(input = input_protein, 
+                                         annotation = annotation_protein,
+                                         global_qvalue_cutoff = global_qvalue_cutoff,
+                                         qvalue_cutoff = qvalue_cutoff,
+                                         pg_qvalue_cutoff = pg_qvalue_cutoff,
+                                         useUniquePeptide = useUniquePeptide,
+                                         removeFewMeasurements = removeFewMeasurements,
+                                         removeOxidationMpeptides = removeOxidationMpeptides,
+                                         removeProtein_with1Feature = removeProtein_with1Feature,
+                                         use_log_file = use_log_file,
+                                         append = append,
+                                         verbose = verbose,
+                                         log_file_path = log_file_path,
+                                         MBR = MBR,
                                          quantificationColumn = quantificationColumn)
     
     msstats_format = list(PTM=ptm_input, PROTEIN=protein_input)
diff --git a/man/DIANNtoMSstatsPTMFormat.Rd b/man/DIANNtoMSstatsPTMFormat.Rd
index 4c130a6..a753850 100644
--- a/man/DIANNtoMSstatsPTMFormat.Rd
+++ b/man/DIANNtoMSstatsPTMFormat.Rd
@@ -51,21 +51,27 @@ in \code{protein_id_col}. The protein names in these two columns must match in
 order to join the FASTA file with the DIA-NN output. Default is "uniprot_ac"
 for uniprot ID. For uniprot mnemonic ID, use "entry_name"}
 
-\item{global_qvalue_cutoff}{The global qvalue cutoff. Default is 0.01.}
+\item{global_qvalue_cutoff}{The qvalue cutoff for the Q.Value column, i.e.
+the run-specific precursor q-value. Default is 0.01.}
 
-\item{qvalue_cutoff}{local qvalue cutoff for library. Default is 0.01.}
+\item{qvalue_cutoff}{If MBR is false, the qvalue cutoff for the Global.Q.Value
+column, i.e. global precursor q-value.  If MBR is true, the qvalue cutoff for the
+Lib.Q.Value column, i.e. the q-value for the library created after the first MBR pass.
+Default is 0.01.}
 
-\item{pg_qvalue_cutoff}{local qvalue cutoff for protein groups Run should be
-the same as filename. Default is 0.01.}
+\item{pg_qvalue_cutoff}{If MBR is false, the qvalue cutoff for the Global.PG.Q.Value
+column, i.e. the global q-value for the protein group.  If MBR is true, the
+qvalue cutoff for the Lib.PG.Q.Value column, i.e. the protein group q-value for
+the library created after the first MBR pass. Run should be the same as filename.
+Default is 0.01.}
 
-\item{useUniquePeptide}{logical, if TRUE (default) removes peptides that are assigned for more than one proteins.
-We assume to use unique peptide for each protein.}
+\item{useUniquePeptide}{should unique pepties be removed}
 
-\item{removeFewMeasurements}{TRUE (default) will remove the features that have 1 or 2 measurements within each Run.}
+\item{removeFewMeasurements}{should proteins with few measurements be removed}
 
-\item{removeOxidationMpeptides}{TRUE (default) will remove the peptides including oxidation (M) sequence.}
+\item{removeOxidationMpeptides}{should peptides with oxidation be removed}
 
-\item{removeProtein_with1Feature}{TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.}
+\item{removeProtein_with1Feature}{should proteins with a single feature be removed}
 
 \item{MBR}{True if analysis was done with match between runs}
 
@@ -73,18 +79,19 @@ We assume to use unique peptide for each protein.}
 Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x.
 Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.}
 
-\item{use_log_file}{logical. If TRUE, information about data processing will
-be saved to a file.}
+\item{use_log_file}{logical. If TRUE, information about data processing
+will be saved to a file.}
 
-\item{append}{logical. If TRUE, information about data processing will be
-added to an existing log file.}
+\item{append}{logical. If TRUE, information about data processing will be added
+to an existing log file.}
 
-\item{verbose}{logical. If TRUE, information about data processing wil be
-printed to the console.}
+\item{verbose}{logical. If TRUE, information about data processing wil be printed
+to the console.}
 
 \item{log_file_path}{character. Path to a file to which information about
-data processing will be saved. If not provided, such a file will be created
-automatically. If 'append = TRUE', has to be a valid path to a file.}
+data processing will be saved.
+If not provided, such a file will be created automatically.
+If \code{append = TRUE}, has to be a valid path to a file.}
 }
 \value{
 \code{list} of one or two \code{data.frame} of class \code{MSstatsTMT}, named \code{PTM} and \code{PROTEIN}
@@ -120,7 +127,7 @@ head(msstatsptm_format$PTM)
 # Example DIANN 2.0
 input = system.file("tinytest/raw_data/DIANN/diann_2_ptm.parquet", 
                                         package = "MSstatsPTM")
-input = data.table::fread(input)
+input = arrow::read_parquet(input)
 annot = system.file("tinytest/raw_data/DIANN/annotation_diann_2.0_ptm.csv", 
                                         package = "MSstatsPTM")
 annot = data.table::fread(annot)
@@ -133,7 +140,8 @@ msstatsptm_format = DIANNtoMSstatsPTMFormat(
     protein_id_col = "Protein.Names", 
     fasta_path = fasta_path, 
     fasta_protein_name = "entry_name", 
-    use_log_file = FALSE
+    use_log_file = FALSE,
+    quantificationColumn = "auto"
 )
 
 head(msstatsptm_format$PTM)

From 1fc4003a480cae0e19628fa5176efe3e91dbad18 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Wed, 18 Feb 2026 16:57:56 -0500
Subject: [PATCH 3/5] finalize test dataset

---
 .../raw_data/DIANN/diann_2_ptm.parquet        | Bin 51941 -> 51941 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/inst/tinytest/raw_data/DIANN/diann_2_ptm.parquet b/inst/tinytest/raw_data/DIANN/diann_2_ptm.parquet
index b3b64b0d0cc46a3f2c5682510fb4d0909c760b59..43660978195de4d65dbd8249070ee7aaaad38750 100644
GIT binary patch
delta 136
zcmaDlmHFvZ<_+$QlUFg;Om=5Xo*cu(yV;m2KyUI9gUHFv29BF$4HNjKj<AW^h%qoo
ziY?(_kdzVY;(&7Zux_62&@aIKg;DGWquLQRwGP(F2Lp4tzcez5%8C6s$SAsL^29(@
k?gNZs#~9VRIMf>0CmRNaa!+ak$*()iDB85yGH6W&0B-OqqyPW_

delta 134
zcmaDlmHFvZ<_+$QlMgc{Pj+XlnH<B!yV;m2KyUIL1INkD29cX(4HNjKCb5ayh%qoo
zitS-#kdzVY;(&6OaBQCL&@V9gTp%0kBsR4U*2y;mL%F{+GKtEG{W-`e+BA7(pepwl
iMzJ4^YF!*^=h!A22Ig{4Y68jsJH#luX|rX}nhF3mZ!0SR


From f79372e688ebf4467dbb8f3b4d583d82b1df554c Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Wed, 18 Feb 2026 17:10:38 -0500
Subject: [PATCH 4/5] add arrow as a suggested dependency

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index aa696c5..8307464 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,6 +32,7 @@ Suggests:
     tinytest,
     covr,
     mockery,
+    arrow,
     testthat (>= 3.0.0)
 LazyData: true
 LinkingTo: Rcpp

From 4c2f863d5eced3395c34342e4cf5237a4673b603 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Wed, 25 Feb 2026 18:15:25 -0500
Subject: [PATCH 5/5] fix docs

---
 DESCRIPTION                    | 2 +-
 man/DIANNtoMSstatsPTMFormat.Rd | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8307464..35fc5b7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -23,7 +23,7 @@ Authors@R: c(
 License: Artistic-2.0
 Depends: R (>= 4.3)
 Imports: dplyr, gridExtra, stringr, stats, ggplot2, stringi,
-            grDevices, MSstatsTMT, MSstatsConvert, MSstats,
+            grDevices, MSstatsTMT, MSstatsConvert (>= 1.19.1), MSstats,
             data.table, Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools,
             rlang
 Suggests: 
diff --git a/man/DIANNtoMSstatsPTMFormat.Rd b/man/DIANNtoMSstatsPTMFormat.Rd
index a753850..e2139c0 100644
--- a/man/DIANNtoMSstatsPTMFormat.Rd
+++ b/man/DIANNtoMSstatsPTMFormat.Rd
@@ -62,10 +62,9 @@ Default is 0.01.}
 \item{pg_qvalue_cutoff}{If MBR is false, the qvalue cutoff for the Global.PG.Q.Value
 column, i.e. the global q-value for the protein group.  If MBR is true, the
 qvalue cutoff for the Lib.PG.Q.Value column, i.e. the protein group q-value for
-the library created after the first MBR pass. Run should be the same as filename.
-Default is 0.01.}
+the library created after the first MBR pass. Default is 0.01.}
 
-\item{useUniquePeptide}{should unique pepties be removed}
+\item{useUniquePeptide}{should unique peptides be removed}
 
 \item{removeFewMeasurements}{should proteins with few measurements be removed}