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Beckett_et_al_2026_fsr_functions.R

@@ -1,3 +1,46 @@
+# Function definitions used to analyze fractional synthesis rates for 
+# Beckett et al. (2026) The impact of high fat diet on global protein 
+# abundance and fractional synthetic rate in liver and mammary gland of 
+# peak lactation ICR mice. 
+# 
+# The main user-level function is maxQuantFsr() (line 145). 
+#  
+# Required packages: 
+#   dplyr
+#   ggplot2
+#   gtools
+#   lhs (optional)
+#   magrittr
+#   minpack.lm
+#   mvtnorm
+#   openxlsx
+#   pbapply
+#   readxl
+#   stringr
+#   tibble
+#
+# MIT LICENSE
+# 
+# Copyright © 2026 Nathanael I. Lichti <email: nlichti@purdue.edu>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a 
+# copy of this software and associated documentation files (the “Software”),  
+# to deal in the Software without restriction, including without limitation the  
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or  
+# sell copies of the Software, and to permit persons to whom the Software is  
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in  
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,  
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE  
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER  
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN  
+# THE SOFTWARE.
+
 ## Top-level function: maxQuantFsr ---------------------------------------------
 
 #' Proteome-wide estimation of fractional synthesis rates (FSR)
@@ -3362,7 +3405,7 @@ amino_acids <- data.frame(
 stable_isotopes <- data.frame(
   element = c("C","H","N","O","O","S","S","S","Cl","Br"),
   number = c(13,2,15,17,18,33,34,36,37,81),
-  delta = c(1,1,1,1,2,1,2,3,2,2), # nominal mass difference from monoisotope
+  delta = c(1,1,1,1,2,1,2,4,2,2), # nominal mass difference from monoisotope
   mass = c(
     C = 13.00335483507,     # Carbon 13
     H = 2.01410177812,      # Hydrogen 2 (Deuterium)

Beckett_et_al_2026_fsr_run.R

@@ -2,8 +2,30 @@
 # (2026) The impact of high fat diet on global protein abundance and 
 # fractional synthetic rate in liver and mammary gland of peak lactation 
 # ICR mice.
+#
+# MIT LICENSE
+# 
+# Copyright © 2026 Nathanael I. Lichti <email: nlichti@purdue.edu>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a 
+# copy of this software and associated documentation files (the “Software”),  
+# to deal in the Software without restriction, including without limitation the  
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or  
+# sell copies of the Software, and to permit persons to whom the Software is  
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in  
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,  
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE  
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER  
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN  
+# THE SOFTWARE.
 
-source("fsr_functions.R")
+source("./Beckett_et_al_2026_fsr_functions.R")
 
 liverfsr <- maxQuantFsr(
   mq_folder = "./liver",