diff --git a/DESCRIPTION b/DESCRIPTION
index b7f8e0c02..202ee3d7e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: timaR
 Title: Taxonomically Informed Metabolite Annotation
-Version: 2.8.2
+Version: 2.9.0
 Authors@R: c(
     person("Adriano", "Rutz", , "rutz@imsb.biol.ethz.ch", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0443-9902")),
@@ -18,7 +18,7 @@ Imports:
     crayon (>= 1.5.2),
     docopt (>= 0.7.1),
     dplyr (>= 1.1.2),
-    httr (>= 1.4.6),
+    httr (>= 1.4.7),
     igraph (>= 1.5.1),
     jsonlite (>= 1.8.7),
     MsBackendMgf (>= 1.8.0),
@@ -93,6 +93,7 @@ Collate:
     'extract_spectra.R'
     'fake_annotations_columns.R'
     'fake_sop_columns.R'
+    'filter_annotations.R'
     'get_file.R'
     'get_example_sirius.R'
     'get_gnps_tables.R'
@@ -117,6 +118,7 @@ Collate:
     'prepare_features_edges.R'
     'prepare_features_tables.R'
     'prepare_libraries_adducts.R'
+    'prepare_libraries_rt.R'
     'prepare_libraries_sop_closed.R'
     'prepare_libraries_sop_ecmdb.R'
     'prepare_libraries_sop_lotus.R'
diff --git a/NAMESPACE b/NAMESPACE
index 133d2c56f..f317d7686 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,6 +25,7 @@ export(export_spectra_2)
 export(extract_spectra)
 export(fake_annotations_columns)
 export(fake_sop_columns)
+export(filter_annotations)
 export(get_example_sirius)
 export(get_file)
 export(get_gnps_tables)
@@ -50,6 +51,7 @@ export(prepare_features_components)
 export(prepare_features_edges)
 export(prepare_features_tables)
 export(prepare_libraries_adducts)
+export(prepare_libraries_rt)
 export(prepare_libraries_sop_closed)
 export(prepare_libraries_sop_ecmdb)
 export(prepare_libraries_sop_lotus)
diff --git a/NEWS.md b/NEWS.md
index 03bc297a0..d7ab1f0fd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # timaR
 
+# timaR 2.9.0
+
+* Refactored RT matching (#76)
+
 # timaR 2.8.2
 
 * Change from pbmclapply to pblapply
diff --git a/R/annotate_masses.R b/R/annotate_masses.R
index 94d2ac9d9..84fcb130e 100644
--- a/R/annotate_masses.R
+++ b/R/annotate_masses.R
@@ -7,7 +7,6 @@ utils::globalVariables(
     "delta_min",
     "Distance",
     "error_mz",
-    "error_rt",
     "exact_mass",
     "feature_id",
     "feature_id_dest",
@@ -157,8 +156,8 @@ annotate_masses <-
         20
     )
     stopifnot(
-      "Your rt tolerance must be lower or equal to 0.1" = tolerance_rt <=
-        0.1
+      "Your rt tolerance must be lower or equal to 0.05" = tolerance_rt <=
+        0.05
     )
 
     paths <<- parse_yaml_paths()
@@ -465,8 +464,7 @@ annotate_masses <-
         )
       ) |>
       dplyr::mutate(
-        error_mz = adduct_mass - mz_1,
-        error_rt = NA_real_
+        error_mz = adduct_mass - mz_1
       ) |>
       tidytable::select(
         feature_id,
@@ -474,7 +472,6 @@ annotate_masses <-
         mz,
         score_input,
         error_mz,
-        error_rt,
         exact_mass,
         adduct,
         adduct_mass,
@@ -497,7 +494,6 @@ annotate_masses <-
         score_input,
         library,
         error_mz,
-        error_rt,
         exact_mass
       ) |>
       tidyft::filter(!is.na(exact_mass))
@@ -786,7 +782,6 @@ annotate_masses <-
       tidytable::distinct(
         feature_id,
         error_mz,
-        error_rt,
         structure_name,
         structure_inchikey_2D,
         structure_smiles_2D,
diff --git a/R/annotate_spectra.R b/R/annotate_spectra.R
index a3309cb96..660731990 100644
--- a/R/annotate_spectra.R
+++ b/R/annotate_spectra.R
@@ -7,7 +7,6 @@ utils::globalVariables(
     "paths",
     "precursorMz",
     "presence_ratio",
-    "rtime",
     "score",
     "SLAW_ID",
     "structure_inchikey_2D",
@@ -90,7 +89,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
   df_empty <- data.frame(
     feature_id = NA,
     error_mz = NA,
-    error_rt = NA,
     structure_name = NA,
     structure_inchikey_2D = NA,
     structure_smiles_2D = NA,
@@ -129,15 +127,11 @@ annotate_spectra <- function(input = params$files$spectral$raw,
 
     query_precursors <- spectra@backend@spectraData$precursorMz
     query_spectra <- spectra@backend@peaksData
-    query_rts <- spectra@backend@spectraData$rtime
     ## TODO find a way to have consistency in spectrum IDs
     query_ids <- spectra@backend@spectraData$acquisitionNum
     if (is.null(query_ids)) {
       query_ids <- spectra@backend@spectraData$spectrum_id
     }
-    if (is.null(query_rts)) {
-      query_rts <- rep(NA_real_, length(spectra))
-    }
 
     if (approx == FALSE) {
       log_debug("Reducing library size...")
@@ -195,7 +189,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
                    spectral_lib,
                    query_ids,
                    query_spectra,
-                   query_rts,
                    lib_id,
                    minimal,
                    maximal,
@@ -229,7 +222,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
                     list(
                       "feature_id" = query_ids[[spectrum]],
                       "precursorMz" = precursor,
-                      "rtime" = query_rts[[spectrum]],
                       "target_id" = lib_id[indices][[index]],
                       "score" = as.numeric(score),
                       "count_peaks_matched" = NA_integer_,
@@ -257,7 +249,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
                 spectral_lib = lib_spectra,
                 query_ids = query_ids,
                 query_spectra = query_spectra,
-                query_rts = query_rts,
                 lib_id = lib_id,
                 minimal = minimal,
                 maximal = maximal
@@ -295,10 +286,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
     if (is.null(lib_smiles2D)) {
       lib_smiles2D <- rep(NA_character_, length(spectral_library))
     }
-    lib_rts <- spectral_library@backend@spectraData$rtime
-    if (is.null(lib_rts)) {
-      lib_rts <- rep(NA_real_, length(spectral_library))
-    }
     lib_name <- spectral_library@backend@spectraData$name
     if (is.null(lib_name)) {
       lib_name <- rep(NA_character_, length(spectral_library))
@@ -322,7 +309,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
       "target_inchikey_2D" = lib_inchikey2D,
       "target_smiles" = lib_smiles,
       "target_smiles_2D" = lib_smiles2D,
-      "target_rtime" = lib_rts,
       "target_name" = lib_name,
       "target_formula" = lib_mf,
       "target_exactmass" = lib_mass,
@@ -336,8 +322,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
     df_final <- df_final |>
       tidytable::rowwise() |>
       dplyr::mutate(
-        ## Working in minutes
-        error_rt = (target_rtime - rtime) / 60,
         error_mz = target_precursorMz - precursorMz,
         structure_inchikey_2D = ifelse(
           test = is.na(target_inchikey_2D),
@@ -357,7 +341,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
         c(
           "feature_id",
           "error_mz",
-          "error_rt",
           "structure_name" = "target_name",
           "structure_inchikey_2D",
           "structure_smiles_2D",
diff --git a/R/filter_annotations.R b/R/filter_annotations.R
new file mode 100644
index 000000000..848ec0dbe
--- /dev/null
+++ b/R/filter_annotations.R
@@ -0,0 +1,98 @@
+utils::globalVariables(c("params"))
+
+#' @title Filter annotations
+#'
+#' @description This function filters initial annotations.
+#'
+#' @param annotations Prepared annotations file
+#' @param features Prepared features file
+#' @param rts Prepared retention time library
+#' @param output Output file
+#' @param tolerance_rt Tolerance to filter retention time
+#' @param parameters Params
+#'
+#' @return NULL
+#'
+#' @export
+#'
+#' @examples NULL
+filter_annotations <-
+  function(annotations = params$files$annotations$prepared,
+           features = params$files$features$prepared,
+           rts = params$files$libraries$temporal$prepared,
+           output = params$files$annotations$filtered,
+           tolerance_rt = params$ms$tolerances$rt$minutes,
+           parameters = params) {
+    stopifnot(
+      "Annotations file(s) do(es) not exist" =
+        rep(TRUE, length(annotations)) ==
+          lapply(X = annotations, file.exists)
+    )
+    stopifnot(
+      "Retention time file(s) do(es) not exist" =
+        rep(TRUE, length(rts)) ==
+          lapply(X = rts, file.exists)
+    )
+    stopifnot("Your features file does not exist." = file.exists(features))
+
+    paths <<- parse_yaml_paths()
+    params <<- parameters
+
+    log_debug(x = "... features")
+    features_table <- tidytable::fread(
+      file = features,
+      colClasses = "character",
+      na.strings = c("", "NA")
+    )
+    log_debug(x = "... annotations")
+    annotation_table <- lapply(
+      X = annotations,
+      FUN = tidytable::fread,
+      colClasses = "character",
+      na.strings = c("", "NA")
+    ) |>
+      tidytable::bind_rows()
+    log_debug(x = "... retention times")
+    rt_table <- lapply(
+      X = rts,
+      FUN = tidytable::fread,
+      colClasses = "character",
+      na.strings = c("", "NA")
+    ) |>
+      tidytable::bind_rows() |>
+      tidytable::rename(rt_target = rt)
+
+    log_debug(
+      "Filtering annotations outside of",
+      tolerance_rt * 3,
+      "minutes tolerance"
+    )
+    features_annotated_table <- features_table |>
+      tidytable::left_join(annotation_table) |>
+      tidytable::left_join(rt_table) |>
+      data.frame() |>
+      dplyr::mutate(error_rt = as.numeric(rt) - as.numeric(rt_target)) |>
+      dplyr::arrange(abs(error_rt)) |>
+      tidytable::tidytable() |>
+      tidytable::distinct(-error_rt, -rt_target,
+        .keep_all = TRUE
+      ) |>
+      data.frame() |>
+      ## TODO adapt for types and improve the * 3
+      dplyr::filter(abs(error_rt) <= abs(tolerance_rt * 3) |
+        is.na(error_rt)) |>
+      tidytable::tidytable() |>
+      tidytable::select(-rt_target, -type)
+
+    ## in case some features had a single filtered annotation
+    final_table <- features_table |>
+      tidytable::left_join(features_annotated_table)
+
+    export_params(step = "filter_annotations")
+    export_output(
+      x = final_table,
+      file = output[[1]]
+    )
+
+    return(output[[1]])
+  }
diff --git a/R/parse_cli_params.R b/R/parse_cli_params.R
index 8027ef68d..a18e9d2a1 100644
--- a/R/parse_cli_params.R
+++ b/R/parse_cli_params.R
@@ -59,6 +59,9 @@ parse_cli_params <- function() {
       params$files$annotations$raw$sirius <-
         as.character(arguments$fil_ann_raw_sir)
     }
+    if (!is.null(arguments$fil_ann_fil)) {
+      params$files$annotations$filtered <- as.character(arguments$fil_ann_fil)
+    }
     if (!is.null(arguments$fil_ann_pre)) {
       params$files$annotations$prepared <- as.character(arguments$fil_ann_pre)
     }
@@ -199,12 +202,13 @@ parse_cli_params <- function() {
     if (!is.null(arguments$names_mgf_po)) {
       params$names$mgf$polarity <- as.character(arguments$names_mgf_po)
     }
-    if (!is.null(arguments$names_mgf_pc)) {
-      params$names$mgf$precursor_charge <- as.character(arguments$names_mgf_pc)
-    }
-    if (!is.null(arguments$names_mgf_pm)) {
-      params$names$mgf$precursor_mz <- as.character(arguments$names_mgf_pm)
-    }
+    # if (!is.null(arguments$names_mgf_pc)) {
+    #   params$names$mgf$precursor_charge <-
+    #     as.character(arguments$names_mgf_pc)
+    # }
+    # if (!is.null(arguments$names_mgf_pm)) {
+    #   params$names$mgf$precursor_mz <- as.character(arguments$names_mgf_pm)
+    # }
     if (!is.null(arguments$names_mgf_sm)) {
       params$names$mgf$smiles <- as.character(arguments$names_mgf_sm)
     }
@@ -270,6 +274,9 @@ parse_cli_params <- function() {
     if (!is.null(arguments$too_tax_che)) {
       params$tools$taxonomies$chemical <- as.character(arguments$too_tax_che)
     }
+    if (!is.null(arguments$units_rt)) {
+      params$units$rt <- as.character(arguments$units_rt)
+    }
     if (!is.null(arguments$wei_glo_bio)) {
       params$weights$global$biological <- as.numeric(arguments$wei_glo_bio)
     }
diff --git a/R/prepare_annotations_gnps.R b/R/prepare_annotations_gnps.R
index b167d339e..24274f4fd 100644
--- a/R/prepare_annotations_gnps.R
+++ b/R/prepare_annotations_gnps.R
@@ -5,7 +5,6 @@ utils::globalVariables(
     "count_peaks_explained",
     "count_peaks_matched",
     "error_mz",
-    "error_rt",
     "ExactMass",
     "feature_id",
     "INCHI",
@@ -122,13 +121,11 @@ prepare_annotations_gnps <-
         dplyr::mutate(
           error_mz = as.numeric(MZErrorPPM) *
             1E-6 *
-            as.numeric(Precursor_MZ),
-          error_rt = NA
+            as.numeric(Precursor_MZ)
         ) |>
         tidytable::select(
           feature_id = `#Scan#`,
           error_mz = MassDiff,
-          error_rt,
           library = LibraryName,
           structure_name = Compound_Name,
           score_input = MQScore,
diff --git a/R/prepare_annotations_sirius.R b/R/prepare_annotations_sirius.R
index f4cbb3187..721dce8e0 100644
--- a/R/prepare_annotations_sirius.R
+++ b/R/prepare_annotations_sirius.R
@@ -5,7 +5,6 @@ utils::globalVariables(
     "count_peaks_matched",
     "CSI:FingerIDScore",
     "error_mz",
-    "error_rt",
     "explainedIntensity",
     "feature_id",
     "id",
@@ -251,7 +250,6 @@ prepare_annotations_sirius <-
         tidytable::left_join(canopus_npc_prepared) |>
         tidytable::distinct() |>
         tidyft::mutate(
-          error_rt = NA,
           structure_taxonomy_classyfire_chemontid = NA,
           structure_taxonomy_classyfire_01kingdom = NA,
           ## mirror spectral match
diff --git a/R/prepare_annotations_spectra.R b/R/prepare_annotations_spectra.R
index 947d936a6..b59af5397 100644
--- a/R/prepare_annotations_spectra.R
+++ b/R/prepare_annotations_spectra.R
@@ -3,7 +3,6 @@ utils::globalVariables(
     "count_peaks_explained",
     "count_peaks_matched",
     "error_mz",
-    "error_rt",
     "feature_id",
     "params",
     "score",
@@ -109,7 +108,6 @@ prepare_annotations_spectra <-
       tidytable::distinct(
         feature_id,
         error_mz,
-        error_rt,
         structure_name,
         structure_inchikey_2D,
         structure_smiles_2D,
diff --git a/R/prepare_libraries_rt.R b/R/prepare_libraries_rt.R
new file mode 100644
index 000000000..5d3a8c00e
--- /dev/null
+++ b/R/prepare_libraries_rt.R
@@ -0,0 +1,305 @@
+#' @title Prepare libraries of retention times
+#'
+#' @description This function prepares retention times libraries
+#'    to be used for later
+#'
+#' @param mgf_exp MGF containing experimental retention times
+#' @param mgf_is MGF containing in silico predicted retention times
+#' @param temp_exp File containing experimental retention times
+#' @param temp_is File containing in silico predicted retention times
+#' @param output Output file
+#' @param library Library containing the keys
+#' @param col_ik Name of the InChIKey in mgf
+#' @param col_rt Name of the retention time in mgf
+#' @param col_sm Name of the SMILES in mgf
+#' @param name_inchikey Name of the InChIKey in file
+#' @param name_rt Name of the retention time in file
+#' @param name_smiles Name of the SMILES in file
+#' @param unit_rt Unit of the retention time. Must be "seconds" or "minutes"
+#' @param parameters Params
+#'
+#' @return NULL
+#'
+#' @export
+#'
+#' @examples NULL
+prepare_libraries_rt <-
+  function(mgf_exp = params$files$libraries$spectral$exp,
+           mgf_is = params$files$libraries$spectral$is,
+           temp_exp = params$files$libraries$temporal$exp,
+           temp_is = params$files$libraries$temporal$is,
+           output = params$files$libraries$temporal$prepared,
+           library = paths$data$interim$libraries$sop$merged$keys,
+           col_ik = params$names$mgf$inchikey,
+           col_rt = params$names$mgf$retention_time,
+           col_sm = params$names$mgf$smiles,
+           name_inchikey = params$names$inchikey,
+           name_rt = params$names$rt,
+           name_smiles = params$names$smiles,
+           unit_rt = params$units$rt,
+           parameters = params) {
+    stopifnot("Your library file does not exist." = file.exists(library))
+
+    params <<- parameters
+
+    ## default transforms from `Spectra`
+    if (col_rt == "RTINSECONDS") {
+      col_rt <- "rtime"
+    }
+    if (col_sm == "SMILES") {
+      col_sm <- "smiles"
+    }
+
+    ## TODO improve
+    if (length(mgf_exp$neg) == 0) {
+      mgf_exp$neg <- NULL
+    }
+    if (length(mgf_exp$pos) == 0) {
+      mgf_exp$pos <- NULL
+    }
+    if (length(mgf_exp) == 0) {
+      mgf_exp <- NULL
+    }
+    if (length(mgf_is$neg) == 0) {
+      mgf_is$neg <- NULL
+    }
+    if (length(mgf_is$pos) == 0) {
+      mgf_is$pos <- NULL
+    }
+    if (length(mgf_is) == 0) {
+      mgf_is <- NULL
+    }
+    if (length(temp_exp) == 0) {
+      temp_exp <- NULL
+    }
+    if (length(temp_is) == 0) {
+      temp_is <- NULL
+    }
+
+    rts_from_mgf <-
+      function(mgf) {
+        log_debug("Importing spectra ...")
+        spectra <- mgf |>
+          lapply(FUN = import_spectra)
+        log_debug("Extracting retention times...")
+        ## TODO refactor to avoid pos neg
+        rts <-
+          tidytable::bind_rows(
+            spectra$neg@backend@spectraData |>
+              data.frame() |>
+              tidytable::tidytable(),
+            spectra$pos@backend@spectraData |>
+              data.frame() |>
+              tidytable::tidytable()
+          ) |>
+          tidytable::select(tidytable::any_of(c(
+            rt = col_rt,
+            inchikey = col_ik,
+            smiles = col_sm
+          )))
+        return(rts)
+      }
+    rts_from_tab <-
+      function(tab) {
+        log_debug("Importing file ...")
+        rts <- tab |>
+          lapply(FUN = tidytable::fread) |>
+          tidytable::bind_rows() |>
+          tidytable::select(any_of(
+            c(
+              rt = name_rt,
+              inchikey = name_inchikey,
+              smiles = name_smiles
+            )
+          ))
+        return(rts)
+      }
+    polish_df <-
+      function(df,
+               type = "experimental",
+               unit = unit_rt) {
+        df_polished <- df |>
+          data.frame() |>
+          dplyr::mutate(type = type) |>
+          dplyr::rowwise() |>
+          dplyr::mutate(rt = ifelse(unit == "seconds",
+            yes = rt / 60,
+            no = rt
+          )) |>
+          dplyr::bind_rows(data.frame(
+            inchikey = NA_character_,
+            smiles = NA_character_
+          )) |>
+          dplyr::filter(!is.na(as.numeric(rt))) |>
+          dplyr::distinct() |>
+          tidytable::tidytable()
+        return(df_polished)
+      }
+    complete_df <- function(df, library = keys) {
+      log_debug(
+        "There are",
+        nrow(df |>
+          dplyr::filter(is.na(inchikey))),
+        "entries without InChIKey.",
+        "We would recommend you adding them but will try completing."
+      )
+      log_debug("Completing with existing metadata...")
+      df_completed_smiles <- df |>
+        tidytable::inner_join(library, by = c("smiles" = "smiles"))
+      df_empty_smiles <- df |>
+        tidytable::anti_join(library, by = c("smiles" = "smiles"))
+      log_debug(
+        "There are still",
+        nrow(df_empty_smiles),
+        "entries without InChIKey.",
+        "We will query them on the fly, this might take some time."
+      )
+      ## TODO change with a small dependency
+      smiles <- unique(df_empty_smiles$smiles)
+      get_inchikey <- function(smiles, toolkit = "rdkit") {
+        url <- paste0(
+          "https://api.naturalproducts.net/latest/convert/inchikey?smiles=",
+          URLencode(smiles),
+          "&toolkit=",
+          toolkit
+        )
+        tryCatch(
+          expr = jsonlite::fromJSON(txt = url),
+          error = function(e) {
+            return(NA_character_)
+          }
+        )
+      }
+      inchikey <- pbapply::pblapply(
+        X = smiles,
+        FUN = get_inchikey
+      ) |>
+        as.character()
+      df_empty_smiles <- df_empty_smiles |>
+        tidytable::select(-inchikey) |>
+        tidytable::left_join(tidytable::tidytable(
+          smiles,
+          inchikey
+        ))
+
+      df_completed <- df_completed_smiles |>
+        tidytable::bind_rows(df_empty_smiles) |>
+        tidyft::mutate_vars(
+          is.character,
+          .func = function(x) {
+            tidytable::na_if(x, "NA")
+          }
+        )
+      df_completed <- df_completed |>
+        data.frame() |>
+        dplyr::mutate(
+          structure_smiles = smiles,
+          structure_inchikey = tidytable::coalesce(
+            inchikey,
+            inchikey.x,
+            inchikey.y
+          ),
+        ) |>
+        tidytable::tidytable() |>
+        tidytable::select(
+          rt,
+          structure_smiles,
+          structure_inchikey,
+          type
+        ) |>
+        tidytable::distinct()
+      log_debug(
+        "There were still",
+        nrow(df_completed |>
+          dplyr::filter(is.na(
+            structure_inchikey
+          ))),
+        "entries for which no InChIKey could not be found in the end."
+      )
+      return(df_completed)
+    }
+
+    keys <- library |>
+      tidytable::fread(select = c(
+        "structure_inchikey",
+        "structure_smiles"
+      )) |>
+      tidytable::distinct() |>
+      tidytable::select(
+        inchikey = structure_inchikey,
+        smiles = structure_smiles
+      )
+
+    empty_df <- tidytable::tidytable(
+      rt = NA_real_,
+      structure_smiles = NA_character_,
+      structure_inchikey = NA_character_,
+      type = NA_character_
+    )
+
+    ## from mgf
+    if (!is.null(mgf_exp)) {
+      rts_exp_1 <- mgf_exp |>
+        rts_from_mgf() |>
+        polish_df() |>
+        complete_df()
+    } else {
+      rts_exp_1 <- empty_df
+    }
+    if (!is.null(mgf_is)) {
+      rts_is_1 <- mgf_is |>
+        rts_from_mgf() |>
+        polish_df(type = "predicted") |>
+        complete_df()
+    } else {
+      rts_is_1 <- empty_df
+    }
+
+    ## from csv
+    if (!is.null(temp_exp)) {
+      rts_exp_2 <- temp_exp |>
+        rts_from_tab() |>
+        polish_df() |>
+        complete_df()
+    } else {
+      rts_exp_2 <- empty_df
+    }
+    if (!is.null(temp_is)) {
+      rts_is_2 <- temp_is |>
+        rts_from_tab() |>
+        polish_df(type = "predicted") |>
+        complete_df()
+    } else {
+      rts_is_2 <- empty_df
+    }
+
+    rts <- dplyr::bind_rows(
+      rts_exp_1,
+      rts_exp_2,
+      rts_is_1,
+      rts_is_2
+    ) |>
+      dplyr::filter(!is.na(as.numeric(rt))) |>
+      dplyr::filter(!is.na((structure_inchikey))) |>
+      dplyr::select(-structure_smiles) |>
+      dplyr::distinct() |>
+      dplyr::mutate(structure_inchikey_2D = gsub(
+        pattern = "-.*",
+        replacement = "",
+        x = structure_inchikey
+      )) |>
+      ## TODO REMINDER FOR NOW
+      dplyr::select(-structure_inchikey)
+
+    if (nrow(rts) == 0) {
+      log_debug("No retention time library found, returning an empty table.")
+      rts <- tidytable::tidytable(
+        rt = NA_real_,
+        structure_inchikey_2D = NA_character_,
+        type = NA_character_
+      )
+    }
+    export_params(step = "prepare_libraries_rt")
+    export_output(x = rts, file = output)
+    return(output)
+  }
diff --git a/R/select_annotations_columns.R b/R/select_annotations_columns.R
index 8060ace66..127d1bfaf 100644
--- a/R/select_annotations_columns.R
+++ b/R/select_annotations_columns.R
@@ -59,7 +59,6 @@ select_annotations_columns <- function(df,
     tidytable::select(
       feature_id,
       error_mz,
-      error_rt,
       structure_name,
       # structure_inchikey,
       structure_inchikey_2D,
diff --git a/R/weight_annotations.R b/R/weight_annotations.R
index ecda52e53..5b348bbfd 100644
--- a/R/weight_annotations.R
+++ b/R/weight_annotations.R
@@ -8,7 +8,7 @@ utils::globalVariables(
 
 #' @title Weight annotations
 #'
-#' @description This function weights initial annotations.
+#' @description This function weights annotations.
 #'
 #' @include clean_bio.R
 #' @include clean_chemo.R
@@ -25,7 +25,6 @@ utils::globalVariables(
 #' @param annotations Prepared annotations file
 #' @param components Prepared components file
 #' @param edges Prepared edges file
-#' @param features Prepared features file
 #' @param taxa Prepared taxed features file
 #' @param output Output file
 #' @param candidates_initial Number of initial candidates to keep
@@ -112,7 +111,7 @@ weight_annotations <-
              merged$
              structures$
              dd_ddd,
-           annotations = params$files$annotations$prepared,
+           annotations = params$files$annotations$filtered,
            components = params$
              files$
              networks$
@@ -120,7 +119,6 @@ weight_annotations <-
              components$
              prepared,
            edges = params$files$networks$spectral$edges$prepared,
-           features = params$files$features$prepared,
            taxa = params$files$taxa$prepared,
            output = params$files$annotations$processed,
            candidates_initial = params$annotations$candidates$initial,
@@ -175,19 +173,6 @@ weight_annotations <-
     params <<- parameters
 
     log_debug(x = "... files ...")
-    log_debug(x = "... features")
-    features_table <- tidytable::fread(
-      file = features,
-      colClasses = "character",
-      na.strings = c("", "NA")
-    )
-    log_debug(x = "... components")
-    components_table <- tidytable::fread(
-      file = components,
-      colClasses = "character",
-      na.strings = c("", "NA")
-    )
-
     log_debug(x = "... annotations")
     annotation_table <- lapply(
       X = annotations,
@@ -197,21 +182,28 @@ weight_annotations <-
     ) |>
       tidytable::bind_rows()
 
-    log_debug(x = "... metadata_table_biological_annotation")
-    taxed_features_table <- tidytable::fread(
-      file = taxa,
+    log_debug(x = "... components")
+    components_table <- tidytable::fread(
+      file = components,
       colClasses = "character",
       na.strings = c("", "NA")
     )
 
-    log_debug(x = "... edges table")
+    log_debug(x = "... edges")
     edges_table <- tidytable::fread(
       file = edges,
       colClasses = "character",
       na.strings = c("", "NA")
     )
 
-    log_debug(x = "... structure-organism pairs table")
+    log_debug(x = "... taxa")
+    taxed_features_table <- tidytable::fread(
+      file = taxa,
+      colClasses = "character",
+      na.strings = c("", "NA")
+    )
+
+    log_debug(x = "... structure-organism pairs")
     structure_organism_pairs_table <-
       tidytable::fread(
         file = library,
@@ -229,6 +221,10 @@ weight_annotations <-
         na.strings = c("", "NA")
       ))
 
+    log_debug(x = "... features")
+    features_table <- annotation_table |>
+      tidytable::distinct(feature_id, rt, mz)
+
     if (ms1_only == TRUE) {
       annotation_table <- annotation_table |>
         tidyft::filter(score_input == 0)
diff --git a/codemeta.json b/codemeta.json
index 5f1aba279..e4107ed34 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/taxonomicallyinformedannotation/tima-r",
   "issueTracker": "https://github.com/taxonomicallyinformedannotation/tima-r/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.8.2",
+  "version": "2.9.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -346,7 +346,7 @@
       "@type": "SoftwareApplication",
       "identifier": "httr",
       "name": "httr",
-      "version": ">= 1.4.6",
+      "version": ">= 1.4.7",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -545,7 +545,7 @@
     "taxonomicdistance",
     "specializedmetabolome"
   ],
-  "fileSize": "2595.064KB",
+  "fileSize": "2665.504KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
diff --git a/inst/app/R/save_input.R b/inst/app/R/save_input.R
index 58478c038..37d4df48f 100644
--- a/inst/app/R/save_input.R
+++ b/inst/app/R/save_input.R
@@ -157,13 +157,6 @@ save_input <- function(input) {
     dalton$
     ms2 <-
     shiny::isolate(input$ms_tol_mas_dal_ms2)
-  yamls_params$
-    annotate_spectra$
-    ms$
-    tolerances$
-    rt$
-    minutes <-
-    ms_tol_rt_min
 
   yamls_params$
     create_edges_spectra$
@@ -231,15 +224,16 @@ save_input <- function(input) {
     dalton$
     ms2 <-
     shiny::isolate(input$ms_tol_mas_dal_ms2)
+  yamls_params$create_edges_spectra$names$source <- names_source
+  yamls_params$create_edges_spectra$names$target <- names_target
+
   yamls_params$
-    create_edges_spectra$
+    filter_annotations$
     ms$
     tolerances$
     rt$
     minutes <-
     ms_tol_rt_min
-  yamls_params$create_edges_spectra$names$source <- names_source
-  yamls_params$create_edges_spectra$names$target <- names_target
 
   yamls_params$prepare_features_edges$names$source <- names_source
   yamls_params$prepare_features_edges$names$target <- names_target
@@ -263,6 +257,9 @@ save_input <- function(input) {
   yamls_params$prepare_features_tables$names$rt <-
     shiny::isolate(input$names_rt)
 
+  yamls_params$prepare_libraries_rt$names$rt <-
+    shiny::isolate(input$names_rt_2)
+
   yamls_params$
     prepare_libraries_sop_merged$
     organisms$
diff --git a/inst/app/ui.R b/inst/app/ui.R
index 1e0544f19..82b5f0cb6 100644
--- a/inst/app/ui.R
+++ b/inst/app/ui.R
@@ -618,7 +618,7 @@ ui <- fluidPage(
           ),
         textInput(
           inputId = "names_rt",
-          label = "Name of \"retention time\" variable in the input",
+          label = "Name of \"retention time\" variable in the feature table",
           value = "row retention time"
         ) |>
           shinyhelper::helper(
@@ -630,6 +630,17 @@ ui <- fluidPage(
               "Assumed to be in minutes."
             )
           ),
+        textInput(
+          inputId = "names_rt_2",
+          label = "Name of \"retention time\" variable in the rt library",
+          value = "rt"
+        ) |>
+          shinyhelper::helper(
+            type = "inline",
+            content = c(
+              "Name of the `retention time` column in your rt library file."
+            )
+          ),
         textInput(
           inputId = "names_source",
           label = "Name of \"source IDs\" variable in the input",
diff --git a/inst/params/default/annotate_spectra.yaml b/inst/params/default/annotate_spectra.yaml
index 82c524b15..a09455b7d 100644
--- a/inst/params/default/annotate_spectra.yaml
+++ b/inst/params/default/annotate_spectra.yaml
@@ -75,8 +75,3 @@ ms:
       dalton:
         #' Absolute mass tolerance for MS2 in Dalton. FLOAT
         ms2: 0.01
-
-    #' For retention time.
-    rt:
-      #' Retention time tolerance in minutes. FLOAT
-      minutes: 0.05
diff --git a/inst/params/default/filter_annotations.yaml b/inst/params/default/filter_annotations.yaml
new file mode 100644
index 000000000..bb61b07b9
--- /dev/null
+++ b/inst/params/default/filter_annotations.yaml
@@ -0,0 +1,38 @@
+---
+#' Files.
+files:
+  #' Annotations files.
+  annotations:
+    #' List of filtered annotations. STRING
+    filtered:
+      - data/interim/annotations/example_annotations_filtered.tsv.gz
+
+    #' List of prepared annotations. STRING
+    prepared:
+      - data/interim/annotations/example_ms1_prepared.tsv.gz
+      - data/interim/annotations/example_gnps_prepared.tsv.gz
+      - data/interim/annotations/example_spectral_matches_prepared.tsv.gz
+      - data/interim/annotations/example_sirius_prepared.tsv.gz
+      # - data/interim/annotations/example_exp_rt_prepared.tsv.gz
+
+  #' Features files.
+  features:
+    #' Prepared features file. STRING
+    prepared: data/interim/features/example_features.tsv.gz
+
+  #' Libraries files.
+  libraries:
+    #' Temporal libraries. STRING
+    temporal:
+      #' List of prepared temporal libraries. STRING
+      prepared:
+        - data/interim/libraries/rt/prepared.tsv.gz
+
+#' MS related parameters.
+ms:
+  #' Tolerances.
+  tolerances:
+    #' For retention time.
+    rt:
+      #' Retention time tolerance in minutes. FLOAT
+      minutes: 0.05
\ No newline at end of file
diff --git a/inst/params/default/params.yaml b/inst/params/default/params.yaml
index 3cc751af5..11bdf9987 100644
--- a/inst/params/default/params.yaml
+++ b/inst/params/default/params.yaml
@@ -35,26 +35,8 @@ annotations:
     #' Perform approximative matching without precursor matching? BOOLEAN
     approx: no
 
-    #' Similarity method to be used to compare spectra.
-    #' Currently "gnps", "navdist", "ndotproduct",
-    # "neuclidean", "nspectraangle" supported. STRING
-    method: gnps
-
     #' Thresholds
     thresholds:
-      #' Condition to be used to retain candidates.
-      #' Must be "OR" or "AND".
-      #' Example: Minimum 6 peaks AND 0.2 similarity. STRING
-      condition: OR
-
-      #' For peaks.
-      peaks:
-        #' Minimal shared peaks (absolute). INTEGER
-        absolute: 6
-
-        #' Minimal shared peaks (ratio). FLOAT
-        ratio: 0.2
-
       #' For similarity. FLOAT
       similarity: 0.2
 
@@ -75,6 +57,10 @@ files:
       #' Directory containing the sirius results. STRING
       sirius: data/interim/annotations/example_sirius/
 
+    #' List of filtered annotations. STRING
+    filtered:
+      - data/interim/annotations/example_annotations_filtered.tsv.gz
+
     #' List of prepared annotations. STRING
     prepared:
       - data/interim/annotations/example_gnps_prepared.tsv.gz
@@ -176,6 +162,22 @@ files:
         pos:
           - data/interim/libraries/spectra/is/lotus_pos.rds
 
+    #' Temporal libraries. STRING
+    temporal:
+      #' Experimental libraries
+      exp:
+        #' List of experimental temporal libraries. STRING
+        - data/interim/libraries/rt/internal.tsv
+
+      #' In silico libraries
+      is:
+        #' List of in silico temporal libraries. STRING
+        - data/interim/libraries/rt/predicted.tsv
+
+      #' List of prepared temporal libraries. STRING
+      prepared:
+        - data/interim/libraries/rt/prepared.tsv.gz
+
   #' Networks files.
   networks:
     #' Spectral networks files.
@@ -333,6 +335,9 @@ names:
   #' Name of "filename" variable in the input. STRING
   filename: filename
 
+  #' Name of "InChIKey" variable in the input. STRING
+  inchikey: inchikey
+
   #' Name of fields present in the MGF.
   mgf:
     #' Name of "collision energy" in MGF. STRING
@@ -365,6 +370,9 @@ names:
     #' Name of "polarity" in MGF. STRING
     polarity: IONMODE
 
+    #' Name of "retention time" in MGF. STRING
+    retention_time: ~
+
     #' Name of "SMILES" in MGF. STRING
     smiles: SMILES
 
@@ -389,6 +397,9 @@ names:
   #' Name of "retention time" variable in the input. STRING
   rt: rt
 
+  #' Name of "SMILES" variable in the input. STRING
+  smiles: smiles
+
   #' Name of "source IDs" variable in the input. STRING
   source: CLUSTERID1
 
@@ -450,6 +461,11 @@ tools:
     #' Currently only "npc" or supported. STRING
     chemical: npc
 
+#' Units of the different variables in the input files.
+units:
+  #' Unit of the "retention time" variable in the input files. STRING
+  rt: minutes
+
 #' Weights to apply to each part of the final score.
 weights:
   #' Global weights.
diff --git a/inst/params/default/prepare_libraries_rt.yaml b/inst/params/default/prepare_libraries_rt.yaml
new file mode 100644
index 000000000..d81db8ecf
--- /dev/null
+++ b/inst/params/default/prepare_libraries_rt.yaml
@@ -0,0 +1,64 @@
+---
+#' Files.
+files:
+  #' Libraries files.
+  libraries:
+    #' Spectral libraries. STRING
+    spectral:
+      #' Experimental libraries
+      exp:
+        #' List of negative experimental spectral libraries. STRING
+        neg:
+          - data/interim/libraries/spectra/exp/internal_neg.rds
+
+        #' List of positive experimental spectral libraries. STRING
+        pos:
+          - data/interim/libraries/spectra/exp/internal_pos.rds
+
+      #' In silico libraries
+      is:
+        #' List of negative in silico spectral libraries. STRING
+        neg: []
+
+        #' List of positive in silico spectral libraries. STRING
+        pos: []
+
+    #' Temporal libraries. STRING
+    temporal:
+      #' List of experimental temporal libraries. STRING
+      exp: []
+
+      #' List of in silico temporal libraries. STRING
+      is: []
+
+      #' List of prepared temporal libraries. STRING
+      prepared:
+        - data/interim/libraries/rt/prepared.tsv.gz
+
+#' Names of the different variables in the input files.
+names:
+  #' Name of "InChIKey" variable in the input. STRING
+  inchikey: inchikey
+
+  #' Name of fields present in the MGF.
+  mgf:
+    #' Name of "InChIKey" in MGF. STRING
+    inchikey: ~
+
+    #' Name of "retention time" in MGF. STRING
+    retention_time: RTINSECONDS
+
+    #' Name of "SMILES" in MGF. STRING
+    smiles: SMILES
+
+  #' Name of "retention time" variable in the input. STRING
+  rt: rt
+
+  #' Name of "SMILES" variable in the input. STRING
+  smiles: smiles
+
+#' Units of the different variables in the input files.
+units:
+  #' Unit of the "retention time" variable in the input files. 
+  #' Must be "seconds" or "minutes". STRING
+  rt: seconds
diff --git a/inst/params/default/prepare_libraries_sop_merged.yaml b/inst/params/default/prepare_libraries_sop_merged.yaml
index 8e4f1d3bc..ee08e958b 100644
--- a/inst/params/default/prepare_libraries_sop_merged.yaml
+++ b/inst/params/default/prepare_libraries_sop_merged.yaml
@@ -11,9 +11,6 @@ files:
         - data/interim/libraries/sop/ecmdb_prepared.tsv.gz
         - data/interim/libraries/sop/lotus_prepared.tsv.gz
 
-      #' Merged structure organism pairs library. STRING
-      merged: data/interim/libraries/sop/library.tsv.gz
-
 #' Organisms related parameters.
 organisms:
   #' Organisms filter related parameters.
diff --git a/inst/params/default/weight_annotations.yaml b/inst/params/default/weight_annotations.yaml
index 6aa9f0316..78b485de2 100644
--- a/inst/params/default/weight_annotations.yaml
+++ b/inst/params/default/weight_annotations.yaml
@@ -34,13 +34,9 @@ files:
 
   #' Annotations files.
   annotations:
-    #' List of prepared annotations. STRING
-    prepared:
-      - data/interim/annotations/example_ms1_prepared.tsv.gz
-      - data/interim/annotations/example_gnps_prepared.tsv.gz
-      - data/interim/annotations/example_spectral_matches_prepared.tsv.gz
-      - data/interim/annotations/example_sirius_prepared.tsv.gz
-      # - data/interim/annotations/example_exp_rt_prepared.tsv.gz
+    #' List of filtered annotations. STRING
+    filtered:
+      - data/interim/annotations/example_annotations_filtered.tsv.gz
 
     #' Final results file. STRING
     processed: annotations.tsv
@@ -50,11 +46,6 @@ files:
       #' Merged structure organism pairs library. STRING
       merged: data/interim/libraries/keys.tsv.gz
 
-  #' Features files.
-  features:
-    #' Prepared features file. STRING
-    prepared: data/interim/features/example_features.tsv.gz
-
   #' Networks files.
   networks:
     #' Spectral networks files.
diff --git a/inst/paths.yaml b/inst/paths.yaml
index d88ef637b..039bd6e64 100644
--- a/inst/paths.yaml
+++ b/inst/paths.yaml
@@ -119,6 +119,8 @@ params:
       components: inst/params/default/create_components.yaml
       edges:
         spectra: inst/params/default/create_edges_spectra.yaml
+    filter:
+      annotations: inst/params/default/filter_annotations.yaml
     prepare:
       features:
         components: inst/params/default/prepare_features_components.yaml
@@ -126,6 +128,7 @@ params:
         tables: inst/params/default/prepare_features_tables.yaml
       libraries:
         adducts: inst/params/default/prepare_libraries_adducts.yaml
+        rt: inst/params/default/prepare_libraries_rt.yaml
         sop:
           closed: inst/params/default/prepare_libraries_sop_closed.yaml
           ecmdb: inst/params/default/prepare_libraries_sop_ecmdb.yaml
@@ -150,6 +153,8 @@ params:
       components: inst/params/user/create_components.yaml
       edges:
         spectra: inst/params/user/create_edges_spectra.yaml
+    filter:
+      annotations: inst/params/user/filter_annotations.yaml
     prepare:
       features:
         components: inst/params/user/prepare_features_components.yaml
@@ -157,6 +162,7 @@ params:
         tables: inst/params/user/prepare_features_tables.yaml
       libraries:
         adducts: inst/params/user/prepare_libraries_adducts.yaml
+        rt: inst/params/user/prepare_libraries_rt.yaml
         sop:
           closed: inst/params/user/prepare_libraries_sop_closed.yaml
           ecmdb: inst/params/user/prepare_libraries_sop_ecmdb.yaml
@@ -209,4 +215,4 @@ urls:
     pattern:
       pos: isdb_pos.mgf
       neg: isdb_neg.mgf
-version: 2.8.2
+version: 2.9.0
diff --git a/inst/pipelines/_targets.R b/inst/pipelines/_targets.R
index 862b0cab7..e0feb4eed 100644
--- a/inst/pipelines/_targets.R
+++ b/inst/pipelines/_targets.R
@@ -89,6 +89,13 @@ list(
           par_def_cre_edg_spe <- paths$params$default$create$edges$spectra
         }
       ),
+      tar_file(
+        name = par_def_fil_ann,
+        command = {
+          par_def_fil_ann <-
+            paths$params$default$filter$annotations
+        }
+      ),
       tar_file(
         name = par_def_pre_ann_gnp,
         command = {
@@ -135,6 +142,13 @@ list(
             paths$params$default$prepare$libraries$adducts
         }
       ),
+      tar_file(
+        name = par_def_pre_lib_rt,
+        command = {
+          par_def_pre_lib_rt <-
+            paths$params$default$prepare$libraries$rt
+        }
+      ),
       tar_file(
         name = par_def_pre_lib_sop_clo,
         command = {
@@ -260,6 +274,22 @@ list(
               )
           }
         ),
+        tar_file(
+          name = par_usr_fil_ann,
+          command = {
+            par_usr_fil_ann <-
+              prepare_params(
+                filename = par_fin_par$files$pattern,
+                features = par_fin_par$files$features$raw,
+                spectra = par_fin_par$files$spectral$raw,
+                gnps_job_id = par_fin_par$gnps$id,
+                ms_mode = par_fin_par$ms$polarity,
+                taxon = par_fin_par$organisms$taxon,
+                parameters = par_fin_par,
+                step = "filter_annotations"
+              )
+          }
+        ),
         tar_file(
           name = par_usr_cre_edg_spe,
           command = {
@@ -388,6 +418,22 @@ list(
               )
           }
         ),
+        tar_file(
+          name = par_usr_pre_lib_rt,
+          command = {
+            par_usr_pre_lib_rt <-
+              prepare_params(
+                filename = par_fin_par$files$pattern,
+                features = par_fin_par$files$features$raw,
+                spectra = par_fin_par$files$spectral$raw,
+                gnps_job_id = par_fin_par$gnps$id,
+                ms_mode = par_fin_par$ms$polarity,
+                taxon = par_fin_par$organisms$taxon,
+                parameters = par_fin_par,
+                step = "prepare_libraries_rt"
+              )
+          }
+        ),
         tar_file(
           name = par_usr_pre_lib_sop_clo,
           command = {
@@ -560,6 +606,16 @@ list(
             )
         }
       ),
+      tar_target(
+        name = par_fil_ann,
+        command = {
+          par_fil_ann <-
+            parse_yaml_params(
+              def = par_def_fil_ann,
+              usr = par_usr_fil_ann[1]
+            )
+        }
+      ),
       tar_target(
         name = par_pre_ann_gnp,
         command = {
@@ -630,6 +686,16 @@ list(
             )
         }
       ),
+      tar_target(
+        name = par_pre_lib_rt,
+        command = {
+          par_pre_lib_rt <-
+            parse_yaml_params(
+              def = par_def_pre_lib_rt,
+              usr = par_usr_pre_lib_rt[1]
+            )
+        }
+      ),
       tar_target(
         name = par_pre_lib_sop_clo,
         command = {
@@ -1252,7 +1318,36 @@ list(
           )
         )
       )
-    )
+    ),
+    ## Retention times
+    list(tar_file(
+      name = lib_rt,
+      command = {
+        lib_rt <- prepare_libraries_rt(
+          ## TODO refactor to avoid "pos/neg"
+          mgf_exp = list(
+            "neg" = lib_spe_exp_int_pre_neg,
+            "pos" = lib_spe_exp_int_pre_pos
+          ),
+          mgf_is = list(
+            "neg" = lib_spe_is_lot_pre_neg,
+            "pos" = lib_spe_is_lot_pre_pos
+          ),
+          temp_exp = NULL,
+          temp_is = NULL,
+          output = par_pre_lib_rt$files$libraries$temporal$prepared,
+          library = lib_mer_key,
+          col_ik = par_pre_lib_rt$names$mgf$inchikey,
+          col_rt = par_pre_lib_rt$names$mgf$retention_time,
+          col_sm = par_pre_lib_rt$names$mgf$smiles,
+          name_inchikey = par_pre_lib_rt$names$inchikey,
+          name_rt = par_pre_lib_rt$names$rt,
+          name_smiles = par_pre_lib_rt$names$smiles,
+          unit_rt = par_pre_lib_rt$units$rt,
+          parameters = par_pre_lib_rt
+        )
+      }
+    ))
   ),
   ## Annotations
   list(
@@ -1599,18 +1694,49 @@ list(
     }
   ),
   tar_file(
-    name = ann_pre,
+    name = ann_fil,
     command = {
-      ann_pre <- weight_annotations(
-        library = lib_mer_key,
-        str_2d_3d = lib_mer_str_2d_3d,
+      ann_fil <- filter_annotations(
         annotations = list(
           ann_spe_is_pre,
           ann_ms1_pre_ann
         ),
+        features = fea_pre,
+        rts = lib_rt,
+        output = par_fil_ann$files$annotations$filtered,
+        tolerance_rt = par_fil_ann$ms$tolerances$rt$minutes,
+        parameters = par_fil_ann
+      )
+    }
+  ),
+  tar_file(
+    name = ann_fil_crazy,
+    command = {
+      ann_fil_crazy <- filter_annotations(
+        annotations = list(
+          ann_spe_exp_gnp_pre,
+          ann_spe_exp_int_pre,
+          ann_spe_is_pre,
+          ann_sir_pre,
+          ann_ms1_pre_ann
+        ),
+        features = fea_pre,
+        rts = lib_rt,
+        output = par_fil_ann$files$annotations$filtered,
+        tolerance_rt = par_fil_ann$ms$tolerances$rt$minutes,
+        parameters = par_fil_ann
+      )
+    }
+  ),
+  tar_file(
+    name = ann_pre,
+    command = {
+      ann_pre <- weight_annotations(
+        library = lib_mer_key,
+        str_2d_3d = lib_mer_str_2d_3d,
+        annotations = ann_fil,
         components = fea_com_pre,
         edges = fea_edg_pre,
-        features = fea_pre,
         taxa = tax_pre,
         output = par_wei_ann$files$annotations$processed,
         candidates_initial = par_wei_ann$annotations$candidates$initial,
@@ -1658,16 +1784,9 @@ list(
       ann_pre_crazy <- weight_annotations(
         library = lib_mer_key,
         str_2d_3d = lib_mer_str_2d_3d,
-        annotations = list(
-          ann_spe_exp_gnp_pre,
-          ann_spe_exp_int_pre,
-          ann_spe_is_pre,
-          ann_sir_pre,
-          ann_ms1_pre_ann
-        ),
+        annotations = ann_fil_crazy,
         components = fea_com_pre,
         edges = fea_edg_pre,
-        features = fea_pre,
         taxa = tax_pre,
         output = par_wei_ann$files$annotations$processed,
         candidates_initial = par_wei_ann$annotations$candidates$initial,
@@ -2062,9 +2181,9 @@ list(
       }
     ),
     tar_target(
-      name = def_ann_mas,
+      name = benchmark_def_ann_mas,
       command = {
-        def_ann_mas <- parse_yaml_params(
+        benchmark_def_ann_mas <- parse_yaml_params(
           def = par_def_ann_mas,
           usr = par_def_ann_mas
         )
@@ -2081,21 +2200,21 @@ list(
               "data/interim/benchmark/benchmark_ann_ms1_pos.tsv.gz",
             output_edges =
               "data/interim/benchmark/benchmark_edges_ms1_pos.tsv.gz",
-            name_source = def_ann_mas$names$source,
-            name_target = def_ann_mas$names$target,
+            name_source = benchmark_def_ann_mas$names$source,
+            name_target = benchmark_def_ann_mas$names$target,
             str_2d_3d = lib_mer_str_2d_3d,
             str_met = lib_mer_str_met,
             str_nam = lib_mer_str_nam,
             str_tax_cla = lib_mer_str_tax_cla,
             str_tax_npc = lib_mer_str_tax_npc,
             name = lib_add["pos"],
-            adducts_list = def_ann_mas$ms$adducts,
+            adducts_list = benchmark_def_ann_mas$ms$adducts,
             adducts_masses_list = dic_add,
             neutral_losses_list = dic_neu_los,
             ms_mode = "pos",
-            tolerance_ppm = def_ann_mas$ms$tolerances$mass$ppm$ms1,
-            tolerance_rt = def_ann_mas$ms$tolerances$rt$minutes,
-            parameters = def_ann_mas
+            tolerance_ppm = benchmark_def_ann_mas$ms$tolerances$mass$ppm$ms1,
+            tolerance_rt = benchmark_def_ann_mas$ms$tolerances$rt$minutes,
+            parameters = benchmark_def_ann_mas
           )
       }
     ),
@@ -2110,28 +2229,28 @@ list(
               "data/interim/benchmark/benchmark_ann_ms1_neg.tsv.gz",
             output_edges =
               "data/interim/benchmark/benchmark_edges_ms1_neg.tsv.gz",
-            name_source = def_ann_mas$names$source,
-            name_target = def_ann_mas$names$target,
+            name_source = benchmark_def_ann_mas$names$source,
+            name_target = benchmark_def_ann_mas$names$target,
             str_2d_3d = lib_mer_str_2d_3d,
             str_met = lib_mer_str_met,
             str_nam = lib_mer_str_nam,
             str_tax_cla = lib_mer_str_tax_cla,
             str_tax_npc = lib_mer_str_tax_npc,
             name = lib_add["neg"],
-            adducts_list = def_ann_mas$ms$adducts,
+            adducts_list = benchmark_def_ann_mas$ms$adducts,
             adducts_masses_list = dic_add,
             neutral_losses_list = dic_neu_los,
             ms_mode = "neg",
-            tolerance_ppm = def_ann_mas$ms$tolerances$mass$ppm$ms1,
-            tolerance_rt = def_ann_mas$ms$tolerances$rt$minutes,
-            parameters = def_ann_mas
+            tolerance_ppm = benchmark_def_ann_mas$ms$tolerances$mass$ppm$ms1,
+            tolerance_rt = benchmark_def_ann_mas$ms$tolerances$rt$minutes,
+            parameters = benchmark_def_ann_mas
           )
       }
     ),
     tar_target(
-      name = def_cre_edg_spe,
+      name = benchmark_def_cre_edg_spe,
       command = {
-        def_cre_edg_spe <- parse_yaml_params(
+        benchmark_def_cre_edg_spe <- parse_yaml_params(
           def = par_def_cre_edg_spe,
           usr = par_def_cre_edg_spe
         )
@@ -2143,17 +2262,17 @@ list(
         benchmark_edg_spe_pos <- create_edges_spectra(
           input = benchmark_pre_mgf_pos,
           output = "data/interim/benchmark/benchmark_edges_spe_pos.tsv.gz",
-          name_source = def_cre_edg_spe$names$source,
-          name_target = def_cre_edg_spe$names$target,
-          threshold = def_cre_edg_spe$
+          name_source = benchmark_def_cre_edg_spe$names$source,
+          name_target = benchmark_def_cre_edg_spe$names$target,
+          threshold = benchmark_def_cre_edg_spe$
             annotations$
             ms2$
             thresholds$
             similarity,
-          ppm = def_cre_edg_spe$ms$tolerances$mass$ppm$ms2,
-          dalton = def_cre_edg_spe$ms$tolerances$mass$dalton$ms2,
+          ppm = benchmark_def_cre_edg_spe$ms$tolerances$mass$ppm$ms2,
+          dalton = benchmark_def_cre_edg_spe$ms$tolerances$mass$dalton$ms2,
           qutoff = 0,
-          parameters = def_cre_edg_spe
+          parameters = benchmark_def_cre_edg_spe
         )
       }
     ),
@@ -2163,24 +2282,24 @@ list(
         benchmark_edg_spe_neg <- create_edges_spectra(
           input = benchmark_pre_mgf_neg,
           output = "data/interim/benchmark/benchmark_edges_spe_neg.tsv.gz",
-          name_source = def_cre_edg_spe$names$source,
-          name_target = def_cre_edg_spe$names$target,
-          threshold = def_cre_edg_spe$
+          name_source = benchmark_def_cre_edg_spe$names$source,
+          name_target = benchmark_def_cre_edg_spe$names$target,
+          threshold = benchmark_def_cre_edg_spe$
             annotations$
             ms2$
             thresholds$
             similarity,
-          ppm = def_cre_edg_spe$ms$tolerances$mass$ppm$ms2,
-          dalton = def_cre_edg_spe$ms$tolerances$mass$dalton$ms2,
+          ppm = benchmark_def_cre_edg_spe$ms$tolerances$mass$ppm$ms2,
+          dalton = benchmark_def_cre_edg_spe$ms$tolerances$mass$dalton$ms2,
           qutoff = 0,
-          parameters = def_cre_edg_spe
+          parameters = benchmark_def_cre_edg_spe
         )
       }
     ),
     tar_target(
-      name = def_pre_fea_edg,
+      name = benchmark_def_pre_fea_edg,
       command = {
-        def_cre_edg_spe <- parse_yaml_params(
+        benchmark_def_pre_fea_edg <- parse_yaml_params(
           def = par_def_pre_fea_edg,
           usr = par_def_pre_fea_edg
         )
@@ -2192,9 +2311,9 @@ list(
         benchmark_edg_pre_pos <- prepare_features_edges(
           input = list(benchmark_ann_ms1_pre_pos[[2]], benchmark_edg_spe_pos),
           output = "data/interim/benchmark/benchmark_edges_pos.tsv.gz",
-          name_source = def_pre_fea_edg$names$source,
-          name_target = def_pre_fea_edg$names$target,
-          parameters = def_pre_fea_edg
+          name_source = benchmark_def_pre_fea_edg$names$source,
+          name_target = benchmark_def_pre_fea_edg$names$target,
+          parameters = benchmark_def_pre_fea_edg
         )
       }
     ),
@@ -2204,16 +2323,16 @@ list(
         benchmark_edg_pre_neg <- prepare_features_edges(
           input = list(benchmark_ann_ms1_pre_neg[[2]], benchmark_edg_spe_neg),
           output = "data/interim/benchmark/benchmark_edges_neg.tsv.gz",
-          name_source = def_pre_fea_edg$names$source,
-          name_target = def_pre_fea_edg$names$target,
-          parameters = def_pre_fea_edg
+          name_source = benchmark_def_pre_fea_edg$names$source,
+          name_target = benchmark_def_pre_fea_edg$names$target,
+          parameters = benchmark_def_pre_fea_edg
         )
       }
     ),
     tar_target(
-      name = def_cre_com,
+      name = benchmark_def_cre_edg_com,
       command = {
-        def_cre_edg_spe <- parse_yaml_params(
+        benchmark_def_cre_edg_com <- parse_yaml_params(
           def = par_def_cre_com,
           usr = par_def_cre_com
         )
@@ -2225,7 +2344,7 @@ list(
         benchmark_com_pos <- create_components(
           input = benchmark_edg_pre_pos,
           output = "data/interim/benchmark/benchmark_components_pos.tsv.gz",
-          parameters = def_cre_com
+          parameters = benchmark_def_cre_edg_com
         )
       }
     ),
@@ -2235,14 +2354,14 @@ list(
         benchmark_com_neg <- create_components(
           input = benchmark_edg_pre_neg,
           output = "data/interim/benchmark/benchmark_components_neg.tsv.gz",
-          parameters = def_cre_com
+          parameters = benchmark_def_cre_edg_com
         )
       }
     ),
     tar_target(
-      name = def_pre_fea_com,
+      name = benchmark_def_pre_fea_com,
       command = {
-        def_cre_edg_spe <- parse_yaml_params(
+        benchmark_def_pre_fea_com <- parse_yaml_params(
           def = par_def_pre_fea_com,
           usr = par_def_pre_fea_com
         )
@@ -2259,7 +2378,7 @@ list(
             spectral$
             components$
             prepared,
-          parameters = def_pre_fea_com
+          parameters = benchmark_def_pre_fea_com
         )
       }
     ),
@@ -2274,14 +2393,14 @@ list(
             spectral$
             components$
             prepared,
-          parameters = def_pre_fea_com
+          parameters = benchmark_def_pre_fea_com
         )
       }
     ),
     tar_target(
-      name = def_ann_spe,
+      name = benchmark_def_ann_spe,
       command = {
-        def_cre_edg_spe <- parse_yaml_params(
+        benchmark_def_ann_spe <- parse_yaml_params(
           def = par_def_ann_spe,
           usr = par_def_ann_spe
         )
@@ -2295,12 +2414,13 @@ list(
           library = lib_spe_is_lot_pre_pos,
           polarity = "pos",
           output = "data/interim/benchmark/benchmark_ann_spe_pos.tsv.gz",
-          threshold = def_ann_spe$annotations$ms2$thresholds$similarity,
-          ppm = def_ann_spe$ms$tolerances$mass$ppm$ms2,
-          dalton = def_ann_spe$ms$tolerances$mass$dalton$ms2,
+          threshold =
+            benchmark_def_ann_spe$annotations$ms2$thresholds$similarity,
+          ppm = benchmark_def_ann_spe$ms$tolerances$mass$ppm$ms2,
+          dalton = benchmark_def_ann_spe$ms$tolerances$mass$dalton$ms2,
           qutoff = 0,
-          approx = def_ann_spe$annotations$ms2$approx,
-          parameters = def_ann_spe
+          approx = benchmark_def_ann_spe$annotations$ms2$approx,
+          parameters = benchmark_def_ann_spe
         )
       }
     ),
@@ -2312,19 +2432,20 @@ list(
           library = lib_spe_is_lot_pre_neg,
           polarity = "neg",
           output = "data/interim/benchmark/benchmark_ann_spe_neg.tsv.gz",
-          threshold = def_ann_spe$annotations$ms2$thresholds$similarity,
-          ppm = def_ann_spe$ms$tolerances$mass$ppm$ms2,
-          dalton = def_ann_spe$ms$tolerances$mass$dalton$ms2,
+          threshold =
+            benchmark_def_ann_spe$annotations$ms2$thresholds$similarity,
+          ppm = benchmark_def_ann_spe$ms$tolerances$mass$ppm$ms2,
+          dalton = benchmark_def_ann_spe$ms$tolerances$mass$dalton$ms2,
           qutoff = 0,
-          approx = def_ann_spe$annotations$ms2$approx,
-          parameters = def_ann_spe
+          approx = benchmark_def_ann_spe$annotations$ms2$approx,
+          parameters = benchmark_def_ann_spe
         )
       }
     ),
     tar_target(
-      name = def_pre_ann_spe,
+      name = benchmark_def_pre_ann_spe,
       command = {
-        def_cre_edg_spe <- parse_yaml_params(
+        benchmark_def_pre_ann_spe <- parse_yaml_params(
           def = par_def_pre_ann_spe,
           usr = par_def_pre_ann_spe
         )
@@ -2343,7 +2464,7 @@ list(
           str_nam = lib_mer_str_nam,
           str_tax_cla = lib_mer_str_tax_cla,
           str_tax_npc = lib_mer_str_tax_npc,
-          parameters = def_pre_ann_spe
+          parameters = benchmark_def_pre_ann_spe
         )
       }
     ),
@@ -2360,14 +2481,14 @@ list(
           str_nam = lib_mer_str_nam,
           str_tax_cla = lib_mer_str_tax_cla,
           str_tax_npc = lib_mer_str_tax_npc,
-          parameters = def_pre_ann_spe
+          parameters = benchmark_def_pre_ann_spe
         )
       }
     ),
     tar_target(
-      name = def_wei_ann,
+      name = benchmark_def_wei_ann,
       command = {
-        def_cre_edg_spe <- parse_yaml_params(
+        benchmark_def_wei_ann <- parse_yaml_params(
           def = par_def_wei_ann,
           usr = par_def_wei_ann
         )
@@ -2381,35 +2502,57 @@ list(
           str_2d_3d = lib_mer_str_2d_3d,
           candidates_initial = 500,
           candidates_final = 500,
-          score_biological_domain = def_wei_ann$weights$biological$domain,
-          score_biological_kingdom = def_wei_ann$weights$biological$kingdom,
-          score_biological_phylum = def_wei_ann$weights$biological$phylum,
-          score_biological_class = def_wei_ann$weights$biological$class,
-          score_biological_order = def_wei_ann$weights$biological$order,
-          score_biological_infraorder = def_wei_ann$weights$biological$infraorder,
-          score_biological_family = def_wei_ann$weights$biological$family,
-          score_biological_subfamily = def_wei_ann$weights$biological$subfamily,
-          score_biological_tribe = def_wei_ann$weights$biological$tribe,
-          score_biological_subtribe = def_wei_ann$weights$biological$subtribe,
-          score_biological_genus = def_wei_ann$weights$biological$genus,
-          score_biological_subgenus = def_wei_ann$weights$biological$subgenus,
-          score_biological_species = def_wei_ann$weights$biological$species,
-          score_biological_subspecies = def_wei_ann$weights$biological$subspecies,
-          score_biological_variety = def_wei_ann$weights$biological$variety,
-          score_chemical_cla_kingdom = def_wei_ann$weights$chemical$cla$kingdom,
+          score_biological_domain =
+            benchmark_def_wei_ann$weights$biological$domain,
+          score_biological_kingdom =
+            benchmark_def_wei_ann$weights$biological$kingdom,
+          score_biological_phylum =
+            benchmark_def_wei_ann$weights$biological$phylum,
+          score_biological_class =
+            benchmark_def_wei_ann$weights$biological$class,
+          score_biological_order =
+            benchmark_def_wei_ann$weights$biological$order,
+          score_biological_infraorder =
+            benchmark_def_wei_ann$weights$biological$infraorder,
+          score_biological_family =
+            benchmark_def_wei_ann$weights$biological$family,
+          score_biological_subfamily =
+            benchmark_def_wei_ann$weights$biological$subfamily,
+          score_biological_tribe =
+            benchmark_def_wei_ann$weights$biological$tribe,
+          score_biological_subtribe =
+            benchmark_def_wei_ann$weights$biological$subtribe,
+          score_biological_genus =
+            benchmark_def_wei_ann$weights$biological$genus,
+          score_biological_subgenus =
+            benchmark_def_wei_ann$weights$biological$subgenus,
+          score_biological_species =
+            benchmark_def_wei_ann$weights$biological$species,
+          score_biological_subspecies =
+            benchmark_def_wei_ann$weights$biological$subspecies,
+          score_biological_variety =
+            benchmark_def_wei_ann$weights$biological$variety,
+          score_chemical_cla_kingdom =
+            benchmark_def_wei_ann$weights$chemical$cla$kingdom,
           score_chemical_cla_superclass =
-            def_wei_ann$weights$chemical$cla$superclass,
-          score_chemical_cla_class = def_wei_ann$weights$chemical$cla$class,
-          score_chemical_cla_parent = def_wei_ann$weights$chemical$cla$parent,
-          score_chemical_npc_pathway = def_wei_ann$weights$chemical$npc$pathway,
+            benchmark_def_wei_ann$weights$chemical$cla$superclass,
+          score_chemical_cla_class =
+            benchmark_def_wei_ann$weights$chemical$cla$class,
+          score_chemical_cla_parent =
+            benchmark_def_wei_ann$weights$chemical$cla$parent,
+          score_chemical_npc_pathway =
+            benchmark_def_wei_ann$weights$chemical$npc$pathway,
           score_chemical_npc_superclass =
-            def_wei_ann$weights$chemical$npc$superclass,
-          score_chemical_npc_class = def_wei_ann$weights$chemical$npc$class,
-          minimal_ms1_bio = def_wei_ann$annotations$ms1$thresholds$biological,
-          minimal_ms1_chemo = def_wei_ann$annotations$ms1$thresholds$chemical,
-          summarise = def_wei_ann$options$summarise,
-          pattern = def_wei_ann$files$pattern,
-          force = def_wei_ann$options$force,
+            benchmark_def_wei_ann$weights$chemical$npc$superclass,
+          score_chemical_npc_class =
+            benchmark_def_wei_ann$weights$chemical$npc$class,
+          minimal_ms1_bio =
+            benchmark_def_wei_ann$annotations$ms1$thresholds$biological,
+          minimal_ms1_chemo =
+            benchmark_def_wei_ann$annotations$ms1$thresholds$chemical,
+          summarise = benchmark_def_wei_ann$options$summarise,
+          pattern = benchmark_def_wei_ann$files$pattern,
+          force = benchmark_def_wei_ann$options$force,
           parameters = def_wei_ann
         )
       }
@@ -2420,7 +2563,6 @@ list(
         benchmark_files_pos <- list(
           components = benchmark_com_pre_pos,
           edges = benchmark_edg_pre_pos,
-          features = benchmark_pre_meta_pos,
           taxa = benchmark_taxed_pos
         )
       }
@@ -2431,7 +2573,6 @@ list(
         benchmark_files_pos <- list(
           components = benchmark_com_pre_neg,
           edges = benchmark_edg_pre_neg,
-          features = benchmark_pre_meta_neg,
           taxa = benchmark_taxed_neg
         )
       }
diff --git a/inst/scripts/docopt/annotate_masses.txt b/inst/scripts/docopt/annotate_masses.txt
index 3febd2e2f..35ef838df 100644
--- a/inst/scripts/docopt/annotate_masses.txt
+++ b/inst/scripts/docopt/annotate_masses.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/annotate_masses.R
 
-Usage: 
+Usage:
   annotate_masses.R [--fil-ann-pre=<fil-ann-pre>] [--fil-lib-sop-mer=<fil-lib-sop-mer>] [--ms-add-neg=<ms-add-neg>] [--ms-add-pos=<ms-add-pos>] [--ms-int-thr-ms1=<ms-int-thr-ms1>] [--ms-pol=<ms-pol>] [--ms-tol-mas-ppm-ms1=<ms-tol-mas-ppm-ms1>] [--ms-tol-mas-dal-ms1=<ms-tol-mas-dal-ms1>] [--ms-tol-rt-min=<ms-tol-rt-min>] [--force=<force>]
 
 Arguments:
diff --git a/inst/scripts/docopt/annotate_spectra.txt b/inst/scripts/docopt/annotate_spectra.txt
index 976a93bd9..d26a6132d 100644
--- a/inst/scripts/docopt/annotate_spectra.txt
+++ b/inst/scripts/docopt/annotate_spectra.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/annotate_spectra.R --fil-spe-raw data/source/examples/spectra.mgf --fil-lib-spe-pos data/interim/libraries/spectra/is/lotus_pos.sqlite --fil-ann-raw-spe data/interim/annotations/example_isdb.tsv.gz --ms-tol-mas-dal-ms2 0.02 --ms-tol-mas-ppm-ms2 10 --ann-ms2-thr-sim 0.2 --ms-int-thr-ms2 0 --ann-ms2-app false
 
-Usage: 
+Usage:
   annotate_spectra.R [--ann-ms2-app=<ann-ms2-app>] [--ann-ms2-thr-sim=<ann-ms2-thr-sim>] [--fil-ann-raw-spe=<fil-ann-raw-spe>] [--fil-lib-spe-neg=<fil-lib-spe-neg>] [--fil-lib-spe-pos=<fil-lib-spe-pos>] [--fil-spe-raw=<fil-spe-raw>] [--ms-int-thr-ms2=<ms-int-thr-ms2>] [--ms-pol=<ms-pol>] [--ms-tol-mas-ppm-ms2=<ms-tol-mas-ppm-ms2>] [--ms-tol-mas-dal-ms2=<ms-tol-mas-dal-ms2>] [--ms-tol-rt-min=<ms-tol-rt-min>]
 
 Arguments:
diff --git a/inst/scripts/docopt/create_components.txt b/inst/scripts/docopt/create_components.txt
index 3b55beef5..a3210f088 100644
--- a/inst/scripts/docopt/create_components.txt
+++ b/inst/scripts/docopt/create_components.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/create_components.R --fil-net-spe-edg-pro data/interim/features/example_edges.tsv.gz --fil-net-spe-com-raw data/interim/features/example_components.tsv.gz
 
-Usage: 
+Usage:
   create_components.R [--fil-net-spe-edg-pro=<fil-net-spe-edg-pro>] [--fil-net-spe-com-raw=<fil-net-spe-com-raw>]
 
 Arguments:
diff --git a/inst/scripts/docopt/create_edges_spectra.txt b/inst/scripts/docopt/create_edges_spectra.txt
index 072608b2b..b126aed6f 100644
--- a/inst/scripts/docopt/create_edges_spectra.txt
+++ b/inst/scripts/docopt/create_edges_spectra.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/create_edges_spectra.R --fil-spe-raw data/source/examples/spectra.mgf --fil-net-spe-edg-raw data/interim/features/example_edges_spectra.tsv.gz --ms-tol-mas-dal-ms2 0.02 --ms-tol-mas-ppm-ms2 10 --ann-ms2-thr-sim 0.2 --ms-int-thr-ms2 0
 
-Usage: 
+Usage:
   create_edges_spectra.R [--ann-ms2-thr-sim=<ann-ms2-thr-sim>] [--fil-net-spe-edg-raw=<fil-net-spe-edg-raw>] [--fil-spe-raw=<fil-spe-raw>] [--ms-int-thr-ms2=<ms-int-thr-ms2>] [--ms-tol-mas-ppm-ms2=<ms-tol-mas-ppm-ms2>] [--ms-tol-mas-dal-ms2=<ms-tol-mas-dal-ms2>] [--ms-tol-rt-min=<ms-tol-rt-min>]
 
 Arguments:
diff --git a/inst/scripts/docopt/filter_annotations.txt b/inst/scripts/docopt/filter_annotations.txt
new file mode 100644
index 000000000..aeb4ae572
--- /dev/null
+++ b/inst/scripts/docopt/filter_annotations.txt
@@ -0,0 +1,17 @@
+You can use this script with the following example:
+  Rscript inst/scripts/filter_annotations.R
+
+Usage:
+  filter_annotations.R [--fil-ann-fil=<fil-ann-fil>] [--fil-ann-pre=<fil-ann-pre>] [--fil-fea-pre=<fil-fea-prer>] [--fil-lib-tem-pre=<fil-lib-tem-pre>] [--ms-tol-rt-min=<ms-tol-rt-min>]
+
+Arguments:  
+  fil-ann-fil                Filtered annotation file. STRING
+  fil-ann-pre                List of prepared annotation file. STRING
+  fil-fea-pre                Prepared features file. STRING
+  fil-lib-tem-pre            List of prepared temporal libraries. STRING
+  
+  ms-tol-rt-min              Retention time tolerance in minutes. FLOAT
+
+Options:
+  -h --help                  Shows this screen.
+  -v --version               Shows version.
\ No newline at end of file
diff --git a/inst/scripts/docopt/prepare_annotations_gnps.txt b/inst/scripts/docopt/prepare_annotations_gnps.txt
index 4df305e9b..80bf3f8b5 100644
--- a/inst/scripts/docopt/prepare_annotations_gnps.txt
+++ b/inst/scripts/docopt/prepare_annotations_gnps.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_annotations_gnps.R --fil-ann-raw-spe data/interim/annotations/example_gnps.tsv --fil-ann-pre data/interim/annotations/example_gnps_prepared.tsv.gz
 
-Usage: 
+Usage:
   prepare_annotations_gnps.R [--=fil-ann-pre<fil-ann-pre>] [--gnps-id=<gnps-id>] [--gnps-workflow=<gnps-workflow>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_annotations_sirius.txt b/inst/scripts/docopt/prepare_annotations_sirius.txt
index 343c083f4..d9c62a76b 100644
--- a/inst/scripts/docopt/prepare_annotations_sirius.txt
+++ b/inst/scripts/docopt/prepare_annotations_sirius.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_annotations_sirius.R --fil-ann-raw-sir data/interim/annotations/example_sirius/ --fil-ann-pre data/interim/annotations/example_sirius_prepared.tsv.gz
 
-Usage: 
+Usage:
   prepare_annotations_sirius.R [--fil-ann-raw-sir=<fil-ann-raw-sir>] [--fil-ann-pre=<fil-ann-pre>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_annotations_spectra.txt b/inst/scripts/docopt/prepare_annotations_spectra.txt
index ba7b67115..95b8e0751 100644
--- a/inst/scripts/docopt/prepare_annotations_spectra.txt
+++ b/inst/scripts/docopt/prepare_annotations_spectra.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
 Rscript inst/scripts/prepare_annotations_spectra.R --fil-ann-raw-spe data/interim/annotations/example_isdb.tsv.gz --fil-ann-pre data/interim/annotations/example_isdb_prepared.tsv.gz
 
-Usage: 
+Usage:
   prepare_annotations_spectra.R [--fil-ann-raw-spe=<fil-ann-raw-spe>] [--fil-ann-pre=<fil-ann-pre>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_features_components.txt b/inst/scripts/docopt/prepare_features_components.txt
index 0172eaadb..ac9e411b4 100644
--- a/inst/scripts/docopt/prepare_features_components.txt
+++ b/inst/scripts/docopt/prepare_features_components.txt
@@ -1,6 +1,6 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_features_components.R --fil-ann-pre data/interim/annotations/example_gnps_prepared.tsv.gz --fil-ann-pre data/interim/annotations/example_isdb_prepared.tsv.gz --fil-ann-pre data/interim/annotations/example_sirius_prepared.tsv.gz --fil-ann-fil data/interim/annotations/example_filled.tsv.gz
-Usage: 
+Usage:
   prepare_features_components.R [--fil-ann-pre=<fil-ann-pre>] [--fil-ann-fil=<fil-ann-fil>] [--fil-net-spe-com-raw=<fil-net-spe-com-raw>] [--too-net-spe-com=<too-net-spe-com>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_features_edges.txt b/inst/scripts/docopt/prepare_features_edges.txt
index 60123510a..c6226f802 100644
--- a/inst/scripts/docopt/prepare_features_edges.txt
+++ b/inst/scripts/docopt/prepare_features_edges.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_features_edges.R --fil-net-spe-edg-pro data/interim/features/example_edges.tsv.gz
 
-Usage: 
+Usage:
   prepare_features_edges.R [--fil-net-spe-edg-raw=<fil-net-spe-edg-raw>] [--fil-net-spe-edg-pro=<fil-net-spe-edg-pro>] [--names-source=<names-source>] [--names-target=<names-target>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_features_tables.txt b/inst/scripts/docopt/prepare_features_tables.txt
index 5885dd93f..3af2ce110 100644
--- a/inst/scripts/docopt/prepare_features_tables.txt
+++ b/inst/scripts/docopt/prepare_features_tables.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_features_tables.R --fil-fea-raw data/source/example_features.csv --fil-fea-pre data/interim/features/example_features.tsv.gz --names-features 'row ID' --names-precursor 'row m/z' --names-rt 'row retention time'
 
-Usage: 
+Usage:
   prepare_features_tables.R [--fil-fea-raw=<fil-fea-raw>] [--fil-fea-pre=<fil-fea-pre>] [--names-features=<names-features>] [--names-precursor=<names-precursor>] [--names-rt=<names-rt>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_libraries_adducts.txt b/inst/scripts/docopt/prepare_libraries_adducts.txt
index 7cc91bf4b..766d8ed06 100644
--- a/inst/scripts/docopt/prepare_libraries_adducts.txt
+++ b/inst/scripts/docopt/prepare_libraries_adducts.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_libraries_adducts.R --fil-lib-add-pro library
 
-Usage: 
+Usage:
   prepare_libraries_adducts.R [--fil-lib-add-pro=<fil-lib-add-pro>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_libraries_rt.txt b/inst/scripts/docopt/prepare_libraries_rt.txt
new file mode 100644
index 000000000..cf74739b5
--- /dev/null
+++ b/inst/scripts/docopt/prepare_libraries_rt.txt
@@ -0,0 +1,25 @@
+You can use this script with the following example:
+Rscript inst/scripts/prepare_libraries_rt.R --fil-lib-spe-neg data/interim/libraries/spectra/exp/internal_neg.sqlite --fil-lib-spe-pos data/interim/libraries/spectra/exp/internal_pos.sqlite --fil-lib-tem-exp data/source/libraries/rt/internal.tsv --fil-lib-tem-is data/source/libraries/rt/predicted.tsv --fil-lib-tem-pre data/interim/libraries/rt/prepared.tsv.gz
+
+Usage:
+  prepare_libraries_rt.R [--fil-lib-spe-neg=<fil-lib-spe-neg>] [--fil-lib-spe-pos=<fil-lib-spe-pos>] [--fil-lib-tem-exp=<fil-lib-tem-exp>] [--fil-lib-tem-is=<fil-lib-tem-is>] [--fil-lib-tem-exp=<fil-lib-tem-exp>] [--fil-lib-tem-pre=<fil-lib-tem-pre>] [--names-inchikey=<names-inchikey>] [--names-mgf-ik=<names-mgf-ik>] [--names-mgf-rt=<names-mgf-rt>] [--names-mgf-sm=<names-mgf-sm>] [--names-rt=<names-rt>] [--names-smiles=<names-smiles>] [--units-rt=<units-rt>]
+
+Arguments:
+  fil-lib-spe-neg            List of negative spectral libraries. STRING
+  fil-lib-spe-pos            List of positive spectral libraries. STRING
+  fil-lib-tem-exp            List of experimental temporal libraries. STRING
+  fil-lib-tem-is             List of in silico temporal libraries. STRING
+  fil-lib-tem-pre            List of prepared temporal libraries. STRING
+
+  names-inchikey             Name of "InChIKey" variable in the input. STRING
+  names-mgf-ik               Name of "InChIKey" in MGF. STRING
+  names-mgf-rt               Name of "retention time" in MGF. STRING
+  names-mgf-sm               Name of "SMILES" in MGF. STRING
+  names-rt                   Name of "retention time" variable in the input. STRING
+  names-smiles               Name of "SMILES" variable in the input. STRING
+
+  units-rt                   Unit of the "retention time" variable in the input. Must be "seconds" or "minutes". STRING
+
+Options:
+  -h --help                  Shows this screen.
+  -v --version               Shows version.
\ No newline at end of file
diff --git a/inst/scripts/docopt/prepare_libraries_sop_closed.txt b/inst/scripts/docopt/prepare_libraries_sop_closed.txt
index 11169616c..a456af84c 100644
--- a/inst/scripts/docopt/prepare_libraries_sop_closed.txt
+++ b/inst/scripts/docopt/prepare_libraries_sop_closed.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_libraries_sop_closed.R --fil-lib-sop-raw-clo ../lotus-processor/data/processed/220226_closed_metadata.csv.gz --fil-lib-sop-pre data/interim/libraries/sop/closed_prepared.tsv.gz
 
-Usage: 
+Usage:
   prepare_libraries_sop_closed.R [--fil-lib-sop-raw-clo=<fil-lib-sop-raw-clo>] [--fil-lib-sop-pre=<fil-lib-sop-pre>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_libraries_sop_ecmdb.txt b/inst/scripts/docopt/prepare_libraries_sop_ecmdb.txt
index 71c0432c2..661cca6e3 100644
--- a/inst/scripts/docopt/prepare_libraries_sop_ecmdb.txt
+++ b/inst/scripts/docopt/prepare_libraries_sop_ecmdb.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_libraries_sop_ecmdb.R --fil-lib-sop-raw-ecm data/source/libraries/sop/ecmdb.json.zip --fil-lib-sop-pre data/interim/libraries/sop/ecmdb_prepared.tsv.gz
 
-Usage: 
+Usage:
   prepare_libraries_sop_ecmdb.R [--fil-lib-sop-raw-ecm=<fil-lib-sop-raw-ecm>] [--fil-lib-sop-pre=<fil-lib-sop-pre>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_libraries_sop_lotus.txt b/inst/scripts/docopt/prepare_libraries_sop_lotus.txt
index c6c159e7c..7a48fc351 100644
--- a/inst/scripts/docopt/prepare_libraries_sop_lotus.txt
+++ b/inst/scripts/docopt/prepare_libraries_sop_lotus.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_libraries_sop_lotus.R --fil-lib-sop-raw-ecm data/source/libraries/sop/lotus.csv.gz --fil-lib-sop-pro data/interim/libraries/sop/lotus_prepared.tsv.gz
 
-Usage: 
+Usage:
   prepare_libraries_sop_ecmdb.R [--fil-lib-sop-raw-ecm=<fil-lib-sop-raw-ecm>] [--fil-lib-sop-pro=<fil-lib-sop-pro>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_libraries_sop_merged.txt b/inst/scripts/docopt/prepare_libraries_sop_merged.txt
index 9a60896fc..843102bc5 100644
--- a/inst/scripts/docopt/prepare_libraries_sop_merged.txt
+++ b/inst/scripts/docopt/prepare_libraries_sop_merged.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_libraries_sop_merged.R --fil-lib-sop-pro data/interim/libraries/sop/lotus_prepared.tsv.gz --fil-lib-sop-mer bitter_db.tsv.gz --org-fil-mod TRUE --org-fil-lev family --org-fil-val 'Simaroubaceae|Gentianaceae'
 
-Usage: 
+Usage:
   prepare_libraries_sop_merged.R [--fil-lib-sop-pro=<fil-lib-sop-pro>] [--fil-lib-sop-mer=<fil-lib-sop-mer>] [--org-fil-mod=<org-fil-mod>] [--org-fil-lev=<org-fil-lev>] [--org-fil-val=<org-fil-val>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_libraries_spectra.txt b/inst/scripts/docopt/prepare_libraries_spectra.txt
index 5e390322d..a28ec7afd 100644
--- a/inst/scripts/docopt/prepare_libraries_spectra.txt
+++ b/inst/scripts/docopt/prepare_libraries_spectra.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
 Rscript inst/scripts/prepare_libraries_spectra.R --fil-lib-spe-raw data/source/libraries/spectra/exp/spectral_lib_mini_with_rt.mgf --fil-lib-spe-pos data/interim/libraries/spectra/exp/internal_pos.sqlite --ms-pol pos
 
-Usage: 
+Usage:
   prepare_libraries_spectra.R [--fil-lib-spe-neg=<fil-lib-spe-neg>] [--fil-lib-spe-pos=<fil-lib-spe-pos>] [--fil-lib-spe-raw=<fil-lib-spe-raw>] [--ms-pol=<ms-pol>] [--names-mgf-ce=<names-mgf-ce>] [--names-mgf-ci=<names-mgf-ci>] [--names-mgf-em=<names-mgf-em>] [--names-mgf-in=<names-mgf-in>] [--names-mgf-io=<names-mgf-io>] [--names-mgf-ik=<names-mgf-ik>] [--names-mgf-il=<names-mgf-il>] [--names-mgf-mf=<names-mgf-mf>] [--names-mgf-na=<names-mgf-na>] [--names-mgf-po=<names-mgf-po>] [--names-mgf-sm=<names-mgf-sm>] [--names-mgf-sn=<names-mgf-sn>] [--names-mgf-si=<names-mgf-si>] [--names-mgf-sp=<names-mgf-sp>] [--names-mgf-sy=<names-mgf-sy>] [--names-mgf-xl=<names-mgf-xl>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_params.txt b/inst/scripts/docopt/prepare_params.txt
index 0b2b03efb..a99710857 100644
--- a/inst/scripts/docopt/prepare_params.txt
+++ b/inst/scripts/docopt/prepare_params.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_params.R
 
-Usage: 
+Usage:
   prepare_params.R  [--fil-pat=<fil-pat>] [--gnps-id=<gnps-id>] [--gnps-workflow=<gnps-workflow>] [--ms-pol=<ms-pol>] [--org-tax=<org-tax>]
 
 Arguments:
diff --git a/inst/scripts/docopt/prepare_taxa.txt b/inst/scripts/docopt/prepare_taxa.txt
index 42da3ae42..771b25494 100644
--- a/inst/scripts/docopt/prepare_taxa.txt
+++ b/inst/scripts/docopt/prepare_taxa.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/prepare_taxa.R --fil-tax-pro data/interim/taxa/example_taxed.tsv.gz --org-can 1 --names-extension TRUE --names-features "row ID" --names-filename filename --names-taxon ATTRIBUTE_species
 
-Usage: 
+Usage:
   prepare_taxa.R [--fil-fea-raw=<fil-fea-raw>] [--fil-tax-raw=<fil-tax-raw>] [--fil-tax-pro=<fil-tax-pro>] [--gnps-id=<gnps-id>] [--names-extension=<names-extension>] [--names-features=<names-features>] [--names-filename=<names-filename>] [--names-taxon=<names-taxon>] [--org-can=<org-can>] [--org-tax=<org-tax>] [--too-met=<too-met>]
 
 Arguments:
diff --git a/inst/scripts/docopt/weight_annotations.txt b/inst/scripts/docopt/weight_annotations.txt
index a5d5823f1..0d2dee493 100644
--- a/inst/scripts/docopt/weight_annotations.txt
+++ b/inst/scripts/docopt/weight_annotations.txt
@@ -1,7 +1,7 @@
 You can use this script with the following example:
   Rscript inst/scripts/weight_annotations.R
 
-Usage: 
+Usage:
   weight_annotations.R [--ann-can-ini=<ann-can-ini>] [--ann-can-fin=<ann-can-fin>] [--ann-ms1only=<ann-ms1only>] [--ann-ms1-thr-bio=<ann-ms1-thr-bio>] [--ann-ms1-thr-che=<ann-ms1-thr-che>] [--ann-ms1-thr-con=<ann-ms1-thr-con>] [--fil-ann-fil=<fil-ann-fil>] [--fil-ann-pro=<fil-ann-pro>] [--fil-lib-sop-mer=<fil-lib-sop-mer>] [--fil-net-spe-edg-pro=<fil-net-spe-edg-pro>] [--fil-tax-pro=<fil-tax-pro>] [--wei-glo-bio=<wei-glo-bio>] [--wei-glo-che=<wei-glo-che>] [--wei-glo-spe=<wei-glo-spe>] [--wei-bio-01=<wei-bio-01>] [--wei-bio-02=<wei-bio-02>] [--wei-bio-03=<wei-bio-03>] [--wei-bio-04=<wei-bio-04>] [--wei-bio-05=<wei-bio-05>] [--wei-bio-06=<wei-bio-06>] [--wei-bio-07=<wei-bio-07>] [--wei-bio-08=<wei-bio-08>] [--wei-bio-09=<wei-bio-09>] [--wei-bio-10=<wei-bio-10>] [--wei-bio-11=<wei-bio-11>] [--wei-bio-12=<wei-bio-12>] [--wei-bio-13=<wei-bio-13>] [--wei-bio-14=<wei-bio-14>] [--wei-bio-15=<wei-bio-15>] [--wei-che-11=<wei-che-11>] [--wei-che-12=<wei-che-12>] [--wei-che-13=<wei-che-13>]  [--wei-che-14=<wei-che-14>] [--wei-che-21=<wei-che-21>] [--wei-che-22=<wei-che-22>] [--wei-che-23=<wei-che-23>] [--summarise=<summarise>] [--force=<force>]
 
 Arguments:
@@ -12,6 +12,7 @@ Arguments:
   ann-ms1-thr-che            Minimal chemical score to keep MS1 only annotation. FLOAT
   ann-ms1-thr-con            Condition to be used to retain candidates. Must be "OR" or "AND". Example: Minimum 0.5 biological AND 0.5 chemical. STRING
   
+  fil-ann-fil                Filtered annotation file. STRING
   fil-ann-pro                Final results file. STRING
   fil-lib-sop-mer            Merged structure organism pairs library. STRING
   fil-net-spe-edg-pro        Prepared edges file. STRING
diff --git a/inst/scripts/filter_annotations.R b/inst/scripts/filter_annotations.R
new file mode 100644
index 000000000..c3b459ac8
--- /dev/null
+++ b/inst/scripts/filter_annotations.R
@@ -0,0 +1,21 @@
+start <- Sys.time()
+
+require(
+  package = "timaR",
+  quietly = TRUE
+)
+
+log_debug(
+  "This script performs",
+  crayon::green("filters annotations"),
+  "based on",
+  crayon::blue("retention time matching")
+)
+log_debug("Authors: ", crayon::green("AR"), "\n")
+log_debug("Contributors: ...")
+
+targets::tar_make(names = matches("^ann_fil"))
+
+end <- Sys.time()
+
+log_debug("Script finished in", crayon::green(format(end - start)))
diff --git a/inst/scripts/prepare_libraries_rt.R b/inst/scripts/prepare_libraries_rt.R
new file mode 100644
index 000000000..4cbb066af
--- /dev/null
+++ b/inst/scripts/prepare_libraries_rt.R
@@ -0,0 +1,22 @@
+start <- Sys.time()
+
+require(
+  package = "timaR",
+  quietly = TRUE
+)
+
+log_debug(
+  "This script",
+  crayon::green(
+    "prepares a library of retention times",
+    "from MGF or tabular data. \n"
+  )
+)
+log_debug("Authors: ", crayon::green("AR"), "\n")
+log_debug("Contributors: ...")
+
+targets::tar_make(names = matches("lib_rt"))
+
+end <- Sys.time()
+
+log_debug("Script finished in", crayon::green(format(end - start)))
diff --git a/man/filter_annotations.Rd b/man/filter_annotations.Rd
new file mode 100644
index 000000000..e61c62d72
--- /dev/null
+++ b/man/filter_annotations.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/filter_annotations.R
+\name{filter_annotations}
+\alias{filter_annotations}
+\title{Filter annotations}
+\usage{
+filter_annotations(
+  annotations = params$files$annotations$prepared,
+  features = params$files$features$prepared,
+  rts = params$files$libraries$temporal$prepared,
+  output = params$files$annotations$filtered,
+  tolerance_rt = params$ms$tolerances$rt$minutes,
+  parameters = params
+)
+}
+\arguments{
+\item{annotations}{Prepared annotations file}
+
+\item{features}{Prepared features file}
+
+\item{rts}{Prepared retention time library}
+
+\item{output}{Output file}
+
+\item{tolerance_rt}{Tolerance to filter retention time}
+
+\item{parameters}{Params}
+}
+\description{
+This function filters initial annotations.
+}
+\examples{
+NULL
+}
diff --git a/man/prepare_libraries_rt.Rd b/man/prepare_libraries_rt.Rd
new file mode 100644
index 000000000..2553765bd
--- /dev/null
+++ b/man/prepare_libraries_rt.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prepare_libraries_rt.R
+\name{prepare_libraries_rt}
+\alias{prepare_libraries_rt}
+\title{Prepare libraries of retention times}
+\usage{
+prepare_libraries_rt(
+  mgf_exp = params$files$libraries$spectral$exp,
+  mgf_is = params$files$libraries$spectral$is,
+  temp_exp = params$files$libraries$temporal$exp,
+  temp_is = params$files$libraries$temporal$is,
+  output = params$files$libraries$temporal$prepared,
+  library = paths$data$interim$libraries$sop$merged$keys,
+  col_ik = params$names$mgf$inchikey,
+  col_rt = params$names$mgf$retention_time,
+  col_sm = params$names$mgf$smiles,
+  name_inchikey = params$names$inchikey,
+  name_rt = params$names$rt,
+  name_smiles = params$names$smiles,
+  unit_rt = params$units$rt,
+  parameters = params
+)
+}
+\arguments{
+\item{mgf_exp}{MGF containing experimental retention times}
+
+\item{mgf_is}{MGF containing in silico predicted retention times}
+
+\item{temp_exp}{File containing experimental retention times}
+
+\item{temp_is}{File containing in silico predicted retention times}
+
+\item{output}{Output file}
+
+\item{library}{Library containing the keys}
+
+\item{col_ik}{Name of the InChIKey in mgf}
+
+\item{col_rt}{Name of the retention time in mgf}
+
+\item{col_sm}{Name of the SMILES in mgf}
+
+\item{name_inchikey}{Name of the InChIKey in file}
+
+\item{name_rt}{Name of the retention time in file}
+
+\item{name_smiles}{Name of the SMILES in file}
+
+\item{unit_rt}{Unit of the retention time. Must be "seconds" or "minutes"}
+
+\item{parameters}{Params}
+}
+\description{
+This function prepares retention times libraries
+to be used for later
+}
+\examples{
+NULL
+}
diff --git a/man/weight_annotations.Rd b/man/weight_annotations.Rd
index c565d040b..087af537e 100644
--- a/man/weight_annotations.Rd
+++ b/man/weight_annotations.Rd
@@ -8,10 +8,9 @@ weight_annotations(
   library = paths$data$interim$libraries$sop$merged$keys,
   org_tax_ott = paths$data$interim$libraries$sop$merged$organisms$taxonomies$ott,
   str_2d_3d = paths$data$interim$libraries$sop$merged$structures$dd_ddd,
-  annotations = params$files$annotations$prepared,
+  annotations = params$files$annotations$filtered,
   components = params$files$networks$spectral$components$prepared,
   edges = params$files$networks$spectral$edges$prepared,
-  features = params$files$features$prepared,
   taxa = params$files$taxa$prepared,
   output = params$files$annotations$processed,
   candidates_initial = params$annotations$candidates$initial,
@@ -63,8 +62,6 @@ weight_annotations(
 
 \item{edges}{Prepared edges file}
 
-\item{features}{Prepared features file}
-
 \item{taxa}{Prepared taxed features file}
 
 \item{output}{Output file}
@@ -160,7 +157,7 @@ match (should be lower than \verb{NPC class})}
 \item{parameters}{Params}
 }
 \description{
-This function weights initial annotations.
+This function weights annotations.
 }
 \examples{
 NULL
diff --git a/tests/testthat/test_functions.R b/tests/testthat/test_functions.R
index cf59d54d2..b6071920f 100644
--- a/tests/testthat/test_functions.R
+++ b/tests/testthat/test_functions.R
@@ -248,6 +248,11 @@ testthat::test_that("Whole process", {
   params <- get_params(step = step)
   prepare_libraries_adducts()
 
+  ### Retention time
+  step <- "prepare_libraries_rt"
+  params <- get_params(step = step)
+  prepare_libraries_rt()
+
   ### Features
   step <- "prepare_features_tables"
   params <- get_params(step = step)
@@ -354,6 +359,11 @@ testthat::test_that("Whole process", {
     output = "data/interim/benchmark/bench_test_out.tsv.gz"
   )
 
+  ## Filter annotations
+  step <- "filter_annotations"
+  params <- get_params(step = step)
+  filter_annotations()
+
   ## Perform TIMA
   step <- "weight_annotations"
   params <- get_params(step = step)
@@ -428,8 +438,8 @@ testthat::test_that("Whole process", {
   arguments$names_mgf_mf <<- "x"
   arguments$names_mgf_na <<- "x"
   arguments$names_mgf_po <<- "x"
-  arguments$names_mgf_pc <<- "x"
-  arguments$names_mgf_pm <<- "x"
+  # arguments$names_mgf_pc <<- "x"
+  # arguments$names_mgf_pm <<- "x"
   arguments$names_mgf_sm <<- "x"
   arguments$names_mgf_sn <<- "x"
   arguments$names_mgf_si <<- "x"
@@ -451,6 +461,7 @@ testthat::test_that("Whole process", {
   arguments$too_net_spe_edg <<- "x"
   arguments$too_tax_bio <<- "x"
   arguments$too_tax_che <<- "x"
+  arguments$units_rt <<- "x"
   arguments$wei_glo_bio <<- "x"
   arguments$wei_glo_che <<- "x"
   arguments$wei_glo_spe <<- "x"
diff --git a/vignettes/II-inputs.Rmd b/vignettes/II-inputs.Rmd
index 18691d4fe..2ea41c229 100644
--- a/vignettes/II-inputs.Rmd
+++ b/vignettes/II-inputs.Rmd
@@ -300,6 +300,34 @@ Before running the corresponding code, do not forget to modify `inst/params/user
 source(file = "inst/scripts/prepare_libraries_adducts.R")
 ```
 
+#### Retention times
+
+The next library you might want is a retention times library.
+This library is **optional**.
+As no standard LC method is shared (for now) among laboratories, this library
+will be heavily laboratory-dependent.
+It could also be a library of in silico predicted retention times.
+
+```{r rts-1, echo=FALSE, message=FALSE, warning=FALSE, out.width="100%"}
+targets::tar_visnetwork(
+  names = starts_with("lib_rt"),
+  exclude = c(
+    contains("benchmark"),
+    contains("par_"),
+    contains("paths")
+  ),
+  targets_only = TRUE,
+  degree_from = 8
+)
+```
+
+We only use the previously generated library to fill up missing InChIKeys.
+Before running the corresponding code, do not forget to modify `inst/params/user/prepare_libraries_rt.yaml`.
+
+```{r adducts-2, results="hide", message=FALSE, warning=FALSE}
+source(file = "inst/scripts/prepare_libraries_rt.R")
+```
+
 #### Spectra
 
 Finally, you need a spectral library to perform MS^2^-based annotation.
diff --git a/vignettes/III-formatting.Rmd b/vignettes/III-formatting.Rmd
index 2338d87e1..87f9ea648 100644
--- a/vignettes/III-formatting.Rmd
+++ b/vignettes/III-formatting.Rmd
@@ -223,11 +223,24 @@ Before running the corresponding code, do not forget to modify `inst/params/user
 source(file = "inst/scripts/prepare_taxa.R")
 ```
 
+## Filter annotations (based on retention time)
+
+This step allows you to filter out the annotation of all the tools used,
+based on your own internal (experimental or predicted) retention times library.
+It is optional. 
+If you do not have one, it will simply group the annotations of all tools. 
+
+Before running the corresponding code, do not forget to modify `inst/params/user/filter_annotations.yaml`.
+
+```{r prepare-taxa, results="hide", message=FALSE, warning=FALSE}
+source(file = "inst/scripts/filter_annotations.R")
+```
+
 You are almost there! See already all the steps accomplished!
 
 ```{r features-all, echo=FALSE, message=FALSE, warning=FALSE, out.width="100%"}
 targets::tar_visnetwork(
-  names = starts_with("fea"),
+  names = matches("^ann"),
   exclude = c(
     contains("benchmark"),
     contains("par_"),