diff --git a/DESCRIPTION b/DESCRIPTION
index 3f5e090..045357a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: MSstatsLiP
 Title: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
-Version: 1.17.0
+Version: 1.17.1
 Date: 2024-3-19
 Description: Tools for LiP peptide and protein significance analysis. Provides 
               functions for summarization, estimation of LiP peptide abundance, 
@@ -31,4 +31,4 @@ BugReports: https://github.com/Vitek-Lab/MSstatsLiP/issues
 Encoding: UTF-8
 LazyData: TRUE
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
diff --git a/R/groupComparisonLiP.R b/R/groupComparisonLiP.R
index 5304b1c..600bb2b 100644
--- a/R/groupComparisonLiP.R
+++ b/R/groupComparisonLiP.R
@@ -13,23 +13,15 @@
 #' @param data list of summarized datasets. Can be output of MSstatsLiP
 #' summarization function \code{\link[MSstatsLiP]{dataSummarizationLiP}}. Must
 #' include dataset named "LiP" as minimum.
-#' @param contrast.matrix comparison between conditions of interests. Default
-#' models full pairwise comparison between all conditions
 #' @param fasta.path a file path to a fasta file that includes the proteins
 #' listed in the data. Default is NULL. Include this parameter to determine
 #' trypticity of peptides in LiP models.
-#' @param log_base base of the logarithm used in dataProcess.
-#' @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 will 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.
 #' @param base start of the file name.
+#' @inheritParams MSstatsPTM::groupComparisonPTM
 #' @return list of modeling results. Includes LiP, PROTEIN, and ADJUSTED LiP
 #'         data.tables with their corresponding model results.
 #' @examples
@@ -92,9 +84,20 @@ groupComparisonLiP <- function(data, contrast.matrix = "pairwise",
                       PROTEIN = data.protein)
 
   ## Model
-  model.data <- groupComparisonPTM(format.data, "LabelFree", contrast.matrix,
-                                   FALSE, "BH", log_base, use_log_file, append,
-                                   verbose, path, base)
+  model.data <- groupComparisonPTM(
+      format.data, 
+      contrast.matrix = contrast.matrix,
+      ptm_label_type = "LF",
+      protein_label_type = "LF",
+      moderated = FALSE, 
+      adj.method = "BH",
+      log_base = log_base,
+      save_fitted_models=TRUE,
+      use_log_file = use_log_file, 
+      append = append,
+      verbose = verbose, 
+      log_file_path = path
+  )
   model.data$ADJUSTED.Model <- model.data$ADJUSTED.Model[!is.na(
     model.data$ADJUSTED.Model$Protein)]
 
diff --git a/man/groupComparisonLiP.Rd b/man/groupComparisonLiP.Rd
index 1ec28bc..a6707c7 100644
--- a/man/groupComparisonLiP.Rd
+++ b/man/groupComparisonLiP.Rd
@@ -29,7 +29,8 @@ models full pairwise comparison between all conditions}
 listed in the data. Default is NULL. Include this parameter to determine
 trypticity of peptides in LiP models.}
 
-\item{log_base}{base of the logarithm used in dataProcess.}
+\item{log_base}{For non-TMT experiments only. The base of the logarithm used
+in summarization.}
 
 \item{use_log_file}{logical. If TRUE, information about data processing
 will be saved to a file.}