diff --git a/R/MSstatsConvert_core_functions.R b/R/MSstatsConvert_core_functions.R
index dc3ab08e..0b6c03c8 100644
--- a/R/MSstatsConvert_core_functions.R
+++ b/R/MSstatsConvert_core_functions.R
@@ -393,8 +393,12 @@ MSstatsPreprocess = function(
 #' 
 #' @param input `data.table` processed by the `MSstatsPreprocess` function
 #' @param feature_columns str, names of columns that define spectral features
-#' @param fill_incomplete if TRUE (default), Intensity values for missing runs
-#' will be added as NA
+#' @param fill_incomplete if TRUE (default), ensures that rows with missing data 
+#' for specific features are added as NA. For example, if the y10 ion of 
+#' peptideA is measured in the "disease" samples but entirely missing for the 
+#' "healthy" samples, rows with NA values will be created for the y10 ion of 
+#' peptideA in the "healthy" group. This process increases the number of 
+#' rows to account for all possible feature-sample combinations.
 #' @param handle_fractions if TRUE (default), overlapping fractions will be resolved
 #' @param fix_missing str, optional. Defaults to NULL, which means no action.
 #' If not NULL, must be one of the options: "zero_to_na" or "na_to_zero".
diff --git a/R/clean_ProteomeDiscoverer.R b/R/clean_ProteomeDiscoverer.R
index fc3cc163..4feba663 100644
--- a/R/clean_ProteomeDiscoverer.R
+++ b/R/clean_ProteomeDiscoverer.R
@@ -141,6 +141,7 @@
 #' @param num_proteins_column column name for number of protein groups passed from user
 #' @param run_column column name for Run ID, depends on PD version
 #' @param channels list of column names for channels
+#' @noRd
 .validatePDTMTInputColumns = function(pd_input, 
                                 protein_id_column, 
                                 num_proteins_column, 
diff --git a/man/MSstatsBalancedDesign.Rd b/man/MSstatsBalancedDesign.Rd
index 3ed646b0..0163e4cc 100644
--- a/man/MSstatsBalancedDesign.Rd
+++ b/man/MSstatsBalancedDesign.Rd
@@ -18,8 +18,12 @@ MSstatsBalancedDesign(
 
 \item{feature_columns}{str, names of columns that define spectral features}
 
-\item{fill_incomplete}{if TRUE (default), Intensity values for missing runs
-will be added as NA}
+\item{fill_incomplete}{if TRUE (default), ensures that rows with missing data
+for specific features are added as NA. For example, if the y10 ion of
+peptideA is measured in the "disease" samples but entirely missing for the
+"healthy" samples, rows with NA values will be created for the y10 ion of
+peptideA in the "healthy" group. This process increases the number of
+rows to account for all possible feature-sample combinations.}
 
 \item{handle_fractions}{if TRUE (default), overlapping fractions will be resolved}
 
diff --git a/man/MSstatsConvert.Rd b/man/MSstatsConvert.Rd
index 095984ad..ab9be157 100644
--- a/man/MSstatsConvert.Rd
+++ b/man/MSstatsConvert.Rd
@@ -2,7 +2,6 @@
 % Please edit documentation in R/utils_MSstatsConvert.R
 \docType{_PACKAGE}
 \name{MSstatsConvert}
-\alias{MSstatsConvert-package}
 \alias{MSstatsConvert}
 \title{MSstatsConvert: An R Package to Convert Data from Mass Spectrometry Signal Processing Tools to MSstats Format}
 \description{
@@ -18,16 +17,3 @@ signal processing tools to a format suitable for statistical analysis with the M
 \code{\link{MSstatsBalancedDesign}} for handling fractions and creating balanced data.
 }
 
-\author{
-\strong{Maintainer}: Mateusz Staniak \email{mtst@mstaniak.pl}
-
-Authors:
-\itemize{
-  \item Devon Kohler \email{kohler.d@northeastern.edu}
-  \item Anthony Wu \email{wu.anthon@northeastern.edu}
-  \item Meena Choi \email{mnchoi67@gmail.com}
-  \item Ting Huang \email{thuang0703@gmail.com}
-  \item Olga Vitek \email{o.vitek@northeastern.edu}
-}
-
-}
diff --git a/man/ProteinProspectortoMSstatsTMTFormat.Rd b/man/ProteinProspectortoMSstatsTMTFormat.Rd
index 927cced9..1c4383ae 100644
--- a/man/ProteinProspectortoMSstatsTMTFormat.Rd
+++ b/man/ProteinProspectortoMSstatsTMTFormat.Rd
@@ -19,8 +19,8 @@ ProteinProspectortoMSstatsTMTFormat(
 )
 }
 \arguments{
-\item{input}{txt report file from Protein Prospector with
-\verb{Keep Replicates} option selected.}
+\item{input}{Input txt peptide report file from Protein Prospector with
+"Keep Replicates", "Mods in Peptide", and "Protein Mods" options selected.}
 
 \item{annotation}{data frame which contains column Run, Fraction,
 TechRepMixture, Mixture, Channel, BioReplicate, Condition.}
diff --git a/man/dot-cleanRawPDMSstats.Rd b/man/dot-cleanRawPDMSstats.Rd
index ac25d1f0..01382df2 100644
--- a/man/dot-cleanRawPDMSstats.Rd
+++ b/man/dot-cleanRawPDMSstats.Rd
@@ -9,7 +9,8 @@
   quantification_column,
   protein_id_column,
   sequence_column,
-  remove_shared
+  remove_shared,
+  run_column = "SpectrumFile"
 )
 }
 \arguments{
diff --git a/man/dot-cleanRawPDTMT.Rd b/man/dot-cleanRawPDTMT.Rd
index e1d77495..9a684b0a 100644
--- a/man/dot-cleanRawPDTMT.Rd
+++ b/man/dot-cleanRawPDTMT.Rd
@@ -9,7 +9,8 @@
   remove_shared = TRUE,
   remove_protein_groups = TRUE,
   protein_id_column = "ProteinAccessions",
-  intensity_columns_regexp = "Abundance"
+  intensity_columns_regexp = "Abundance",
+  run_column = "SpectrumFile"
 )
 }
 \arguments{
diff --git a/man/dot-validatePDTMTInputColumns.Rd b/man/dot-validatePDTMTInputColumns.Rd
deleted file mode 100644
index eb5652b0..00000000
--- a/man/dot-validatePDTMTInputColumns.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/clean_ProteomeDiscoverer.R
-\name{.validatePDTMTInputColumns}
-\alias{.validatePDTMTInputColumns}
-\title{Helper method to validate input has necessary columns}
-\usage{
-.validatePDTMTInputColumns(
-  pd_input,
-  protein_id_column,
-  num_proteins_column,
-  channels
-)
-}
-\arguments{
-\item{pd_input}{data.frame input}
-
-\item{protein_id_column}{column name for protein passed from user}
-
-\item{num_proteins_column}{column name for number of protein groups passed from user}
-
-\item{channels}{list of column names for channels}
-}
-\description{
-Helper method to validate input has necessary columns
-}