Vitek-Lab · tonywu1999 · May 27, 2026 · May 22, 2026 · May 27, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -14,7 +14,6 @@ License: Artistic-2.0
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 biocViews: MassSpectrometry, Proteomics, Software, DataImport, QualityControl
 Depends:
     R (>= 4.0)
@@ -82,3 +81,4 @@ Collate:
     'utils_logging.R'
     'utils_shared_peptides.R'
 VignetteBuilder: knitr
+Config/roxygen2/version: 8.0.0
diff --git a/R/utils_documentation.R b/R/utils_documentation.R
@@ -5,7 +5,11 @@
 #' @param removeFewMeasurements TRUE (default) will remove the features that have 1 or 2 measurements across runs.
 #' @param useUniquePeptide TRUE (default) removes peptides that are assigned for more than one proteins. 
 #' We assume to use unique peptide for each protein.
-#' @param summaryforMultipleRows max or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities. Default is max for label-free converters and sum for TMT converters.
+#' @param summaryforMultipleRows max or sum - when multiple PSMs identify
+#' the same feature within a single MS run (duplicate PSMs), use the
+#' highest (max) or sum of the duplicate intensities. Default is max for
+#' label-free converters and sum for TMT converters. Note that this parameter 
+#' does NOT control collapsing across fractions of the same biological mixture.
 #' @param removeProtein_with1Feature TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
 #' @param removeProtein_with1Peptide TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
 #' @param removeOxidationMpeptides TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.

diff --git a/man/DIAUmpiretoMSstatsFormat.Rd b/man/DIAUmpiretoMSstatsFormat.Rd
diff --git a/man/FragPipetoMSstatsFormat.Rd b/man/FragPipetoMSstatsFormat.Rd
diff --git a/man/MSstatsConvert.Rd b/man/MSstatsConvert.Rd
diff --git a/man/MaxQtoMSstatsFormat.Rd b/man/MaxQtoMSstatsFormat.Rd
diff --git a/man/MaxQtoMSstatsTMTFormat.Rd b/man/MaxQtoMSstatsTMTFormat.Rd
diff --git a/man/MetamorpheusToMSstatsFormat.Rd b/man/MetamorpheusToMSstatsFormat.Rd
diff --git a/man/OpenMStoMSstatsFormat.Rd b/man/OpenMStoMSstatsFormat.Rd
diff --git a/man/OpenSWATHtoMSstatsFormat.Rd b/man/OpenSWATHtoMSstatsFormat.Rd
diff --git a/man/PDtoMSstatsFormat.Rd b/man/PDtoMSstatsFormat.Rd
diff --git a/man/PDtoMSstatsTMTFormat.Rd b/man/PDtoMSstatsTMTFormat.Rd
diff --git a/man/PhilosophertoMSstatsTMTFormat.Rd b/man/PhilosophertoMSstatsTMTFormat.Rd
diff --git a/man/ProgenesistoMSstatsFormat.Rd b/man/ProgenesistoMSstatsFormat.Rd
diff --git a/man/ProteinProspectortoMSstatsTMTFormat.Rd b/man/ProteinProspectortoMSstatsTMTFormat.Rd
diff --git a/man/SpectroMinetoMSstatsTMTFormat.Rd b/man/SpectroMinetoMSstatsTMTFormat.Rd
diff --git a/man/SpectronauttoMSstatsFormat.Rd b/man/SpectronauttoMSstatsFormat.Rd
diff --git a/man/dot-getFullDesign.Rd b/man/dot-getFullDesign.Rd
diff --git a/man/dot-sharedParametersAmongConverters.Rd b/man/dot-sharedParametersAmongConverters.Rd
diff --git a/vignettes/msstats_data_format.Rmd b/vignettes/msstats_data_format.Rmd
@@ -304,13 +304,29 @@ should consists of elements named
 
 # Fractions and balanced design
 
-Finally, after preprocessing, `MSstatsBalancedDesign` function can be applied to 
-handle fractions and create balanced design.
-For label-free and SRM data, it means that fractionation or technical replicates will be detected if these information is not provided. Features measured in multiple fractions (overlapped) will be assigned to a unique fraction. Then, the data will be adjusted so that within each fraction, every feature has a row for certain run. If the intensity value is missing, it will be denoted by `NA`.
-
-For TMT data, a unique fraction will be selected for each overlapped feature and the 
-data will adjusted so that within each run, every feature has a row for each channel.
-If the intensity is missing for a channel, it will be denoted by `NA`.
+Finally, after preprocessing, the `MSstatsBalancedDesign` function can be
+applied to handle fractions and create a balanced design.
+
+For label-free data, fractionation or technical replicates are
+detected if this information is not provided. Features that overlap
+across multiple fractions of the same sample are assigned to a single
+fraction by the following rule: for each feature, the fraction with the
+**largest number of MS runs containing a non-missing measurement** is
+kept. If multiple fractions tie on that count, the tie is broken by
+choosing the fraction with the **highest mean intensity**. The
+remaining fractions' rows for that feature are dropped. The data are
+then adjusted so that within each fraction, every feature has a row
+for each run. If the intensity value is missing, it is denoted by `NA`.
+
+For TMT data, a unique fraction is selected for each overlapped feature
+as well. After fraction selection, the data are adjusted so
+that within each run, every feature has a row for each channel. If
+the intensity is missing for a channel, it is denoted by `NA`.
+
+Note also that this fraction-collapsing logic is distinct from the
+`summaryforMultipleRows` argument on each converter, which only
+combines duplicate PSMs identifying the same feature within a single
+MS run.
 
 ```{r }
 maxquant_balanced = MSstatsBalancedDesign(maxquant_processed, feature_columns)