Refactoring MS1 adducts (#141, #144)

NEWS.md

@@ -4,6 +4,7 @@
 
 * Fix library/adducts confusion (#123)
 * Fix some incorrect adduct differences annotations
+* Refactored adducts / neutral losses / dimers annotation to allow for more flexibility (#141, #144)
 
 # timaR 2.9.5
 

R/annotate_masses.R

@@ -440,9 +440,9 @@ annotate_masses <-
     # TODO dictionary of adducts (example 2H2O in mzmine)
 
     df_addlossed_min <- df_addlossed |>
-      tidytable::distinct(mz_1, label) |>
       tidytable::rowwise() |>
-      tidytable::mutate(mass = calculate_mass_from_adduct(adduct_string = label, mass = mz_1))
+      tidytable::mutate(mass = calculate_mass_from_adduct(adduct_string = label, mass = mz_1)) |>
+      tidytable::ungroup()
 
     ## Safety
     df_addlossed_min_1 <- df_addlossed_min |>
@@ -453,8 +453,11 @@ annotate_masses <-
 
     if (nrow(df_addlossed_min_2) != 0) {
       message("Some adducts were unproperly detected, defaulting to (de)protonated")
-      # TODO
-      df_addlossed_min_2
+      df_addlossed_min_2 <- df_addlossed_min_2 |>
+        tidytable::mutate(label = switch(ms_mode, "pos" = "[M+H]+", "neg" = "[M-H]-")) |>
+        tidytable::rowwise() |>
+        tidytable::mutate(mass = calculate_mass_from_adduct(adduct_string = label, mass = mz_1)) |>
+        tidytable::ungroup()
     }
 
     df_addlossed_rdy <- df_addlossed_min_1 |>
@@ -463,7 +466,7 @@ annotate_masses <-
     # TODO if same, say unrecognized and switch to M+H or M-H by default
 
     log_debug("joining within given mz tol to exact mass library \n")
-    df_addlossed_em <- df_addlossed |>
+    df_addlossed_em <- df_addlossed_rdy |>
       dplyr::inner_join(df_add_em,
         by = dplyr::join_by(
           mz_1 >= value_min,

codemeta.json

@@ -553,7 +553,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "4384.938KB",
+  "fileSize": "4385.035KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

tests/testthat/_snaps/shinytest2/001.json

@@ -46,16 +46,16 @@
     "gnps_workflow": "fbmn",
     "launch": 0,
     "ms_add_neg": [
-      "[1M-(H)2]2-",
-      "[1M-(H)1]1-",
-      "[2M-(H)1]1-"
+      "[M-H2]2-",
+      "[M-H]-",
+      "[2M-H]-"
     ],
     "ms_add_pos": [
-      "[1M+(H)2]2+",
-      "[1M+(H)1]1+",
-      "[1M+(H)4(N)1]1+",
-      "[1M+(Na)1]1+",
-      "[2M+(H)1]1+"
+      "[M+H2]2+",
+      "[M+H]+",
+      "[M+H4N]+",
+      "[M+Na]+",
+      "[2M+H]+"
     ],
     "ms_clu_neg": [
       "H2O",
@@ -74,6 +74,7 @@
     "ms_tol_mas_ppm_ms1": 10,
     "ms_tol_mas_ppm_ms2": 10,
     "ms_tol_rt_min": 0.05,
+    "names_adduct": "best ion",
     "names_extension": true,
     "names_features": "row ID",
     "names_filename": "filename",