diff --git a/DESCRIPTION b/DESCRIPTION
index 8b5e977..7d0bc8e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: proteoM
 Type: Package
 Title: Database Searches of Proteomic Mass-spectrometrirc Data
-Version: 1.2.2.1
+Version: 1.2.3
 Authors@R: 
     person(given = "Qiang",
            family = "Zhang",
diff --git a/R/bin_masses.R b/R/bin_masses.R
index e6358db..67eccad 100644
--- a/R/bin_masses.R
+++ b/R/bin_masses.R
@@ -296,14 +296,11 @@ binTheoSeqs <- function (idxes = NULL, res = NULL, min_mass = 200L,
   
   out_dir <- create_dir(gsub("(^.*/).*$", "\\1", out_path))
   
-  out_nms <- gsub("^.*/(.*)\\.[^\\.].*$", "\\1", out_path) %>%
-    paste(idxes, sep = "_") %>%
-    paste0(".rds")
-  
-  res <- res %>%
-    lapply(attributes) %>%
-    lapply(`[[`, "data")
+  out_nms <- gsub("^.*/(.*)\\.[^\\.].*$", "\\1", out_path)
+  out_nms <- paste0(out_nms, "_", idxes, ".rds")
   
+  res <- lapply(res, attributes)
+  res <- lapply(res, `[[`, "data")
   gc()
   
   n_cores <- local({
diff --git a/R/fastas.R b/R/fastas.R
index 2a4b10a..d1c0eb4 100644
--- a/R/fastas.R
+++ b/R/fastas.R
@@ -120,15 +120,13 @@ load_fasta <- function (fasta = NULL)
   
   oks <- file.exists(fasta)
 
-  if (!all(oks)) {
-    bads <- fasta[!oks]
-    stop("Missing FASTA file(s): \n", paste(bads, collapse = "\n"))
-  }
+  if (!all(oks))
+    stop("Missing FASTA file(s): \n", paste(fasta[!oks], collapse = "\n"))
 
-  lapply(fasta, function (x) read_fasta(x)) %>%
-    do.call(`c`, .) %>%
-    `names<-`(gsub(">", "", names(.))) %>%
-    .[!duplicated(names(.))]
+  ans <- lapply(fasta, function (x) read_fasta(x))
+  ans <- flatten_list(ans)
+  names(ans) <- gsub(">", "", names(ans))
+  ans <- ans[!duplicated(names(ans))]
 }
 
 ### End of also in proteoQ
@@ -155,30 +153,26 @@ load_fasta <- function (fasta = NULL)
 #' fasta_db <- load_fasta2(
 #'               c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
 #'                 "~/proteoM/dbs/fasta/crap/crap.fasta"),
-#'               c("uniprot_acc", "other")
-#' )
+#'               c("uniprot_acc", "other"))
 #'
 #' # Need `acc_pattern` as "crap" is not one of the default acc_type
 #' load_fasta2(
 #'    c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
 #'      "~/proteoM/dbs/fasta/crap/crap.fasta"),
-#'    c("uniprot_acc", "crap")
-#' )
+#'    c("uniprot_acc", "crap"))
 #'
 #' # ok
 #' fasta_db2 <- load_fasta2(
 #'                c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
 #'                  "~/proteoM/dbs/fasta/crap/crap.fasta"),
 #'                c("uniprot_acc", "crap"),
-#'                c("^>..\\|([^\\|]+)\\|[^\\|]+", "(.*)")
-#' )
+#'                c("^>..\\|([^\\|]+)\\|[^\\|]+", "(.*)"))
 #'
 #' fasta_db3 <- load_fasta2(
 #'                c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
 #'                  "~/proteoM/dbs/fasta/crap/crap.fasta"),
 #'                c("my_acc", "crap"),
-#'                c("^>..\\|([^\\|]+)\\|[^\\|]+", "(.*)")
-#' )
+#'                c("^>..\\|([^\\|]+)\\|[^\\|]+", "(.*)"))
 #'
 #' stopifnot(identical(fasta_db, fasta_db2),
 #'           identical(fasta_db, fasta_db3))
@@ -191,10 +185,8 @@ load_fasta2 <- function (fasta = NULL, acc_type = NULL, acc_pattern = NULL)
 
   oks <- file.exists(fasta)
   
-  if (!all(oks)) {
-    bads <- fasta[!oks]
-    stop("Missing FASTA file(s): \n", paste(bads, collapse = "\n"))
-  }
+  if (!all(oks))
+    stop("Missing FASTA file(s): \n", paste(fasta[!oks], collapse = "\n"))
 
   len_f <- length(fasta)
   len_a <- length(acc_type)
@@ -204,8 +196,7 @@ load_fasta2 <- function (fasta = NULL, acc_type = NULL, acc_pattern = NULL)
     stop("More accession types than fasta files.")
 
   if (len_f < len_p) 
-    stop("More acc_pattern types than fasta files.",
-         call. = FALSE)
+    stop("More acc_pattern types than fasta files.")
 
   if (len_a && (len_a < len_f)) {
     warning("More fasta files than accession types; ",
@@ -219,7 +210,7 @@ load_fasta2 <- function (fasta = NULL, acc_type = NULL, acc_pattern = NULL)
     acc_pattern <- rep(acc_pattern[1], len_f)
   }
 
-  if (! (is.null(acc_type) || is.null(acc_pattern))) {
+  if (!(is.null(acc_type) || is.null(acc_pattern))) {
     acc_type <- acc_type
     acc_pattern <- acc_pattern
   } 
@@ -228,10 +219,12 @@ load_fasta2 <- function (fasta = NULL, acc_type = NULL, acc_pattern = NULL)
     acc_pattern <- rep("(.*)", len_f)
   } 
   else if (!is.null(acc_type)) {
-    acc_pattern <- purrr::map_chr(acc_type, find_acc_pattern)
+    acc_pattern <- lapply(acc_type, find_acc_pattern)
+    acc_pattern <- unlist(acc_pattern, recursive = FALSE, use.names = FALSE)
   } 
   else {
-    acc_type <- purrr::map_chr(acc_pattern, find_acc_type)
+    acc_type <- lapply(acc_pattern, find_acc_type)
+    acc_type <- unlist(acc_type, recursive = FALSE, use.names = FALSE)
   }
 
   if (length(acc_pattern) != len_f)
@@ -239,11 +232,11 @@ load_fasta2 <- function (fasta = NULL, acc_type = NULL, acc_pattern = NULL)
   
   # Not to USE.NAMES; otherwise fasta names prefix to accession names
   # this is different to map2 where names are NULL for each fasta_db
-  mapply(function (x, y) read_fasta(x, y), fasta, acc_pattern, 
-         SIMPLIFY = FALSE, USE.NAMES = FALSE) %>%
-    do.call(`c`, .) %>%
-    `names<-`(gsub(">", "", names(.))) %>%
-    .[!duplicated(names(.))]
+  ans <- mapply(function (x, y) read_fasta(x, y), fasta, acc_pattern, 
+                SIMPLIFY = FALSE, USE.NAMES = FALSE)
+  ans <- flatten_list(ans)
+  names(ans) <- gsub(">", "", names(ans))
+  ans <- ans[!duplicated(names(ans))]
 }
 
 
@@ -262,23 +255,16 @@ find_acc_pattern <- function (acc_type)
   if (!acc_type %in% oks)
     stop("`acc_type` is not one of ", paste(oks, collapse = ", "))
 
-  acc_pattern <- if (acc_type == "uniprot_acc") {
+  if (acc_type == "uniprot_acc")
     "^>..\\|([^\\|]+)\\|[^\\|]+"
-  } 
-  else if (acc_type == "uniprot_id") {
+  else if (acc_type == "uniprot_id")
     "^>..\\|[^\\|]+\\|([^ ]+) .*"
-  } 
-  else if (acc_type == "refseq_acc") {
+  else if (acc_type == "refseq_acc")
     "^>([^ ]+?) .*"
-  } 
-  else if (acc_type == "other") {
+  else if (acc_type == "other")
     "(.*)"
-  } 
-  else {
+  else
     stop("Unknown `acc_type`.")
-  }
-
-  invisible(acc_pattern)
 }
 
 
@@ -302,22 +288,16 @@ find_acc_type <- function (acc_pattern)
   pat_rsacc <- "^>([^ ]+?) "
   pat_other <- "(.*)"
 
-  acc_type <- if (acc_pattern == pat_upacc) {
+  if (acc_pattern == pat_upacc)
     "uniprot_acc"
-  } 
-  else if (acc_pattern == pat_upid) {
+  else if (acc_pattern == pat_upid)
     "uniprot_id"
-  } 
-  else if (acc_pattern == pat_rsacc) {
+  else if (acc_pattern == pat_rsacc)
     "refseq_acc"
-  } 
-  else if (acc_pattern == pat_other) {
+  else if (acc_pattern == pat_other)
     "other"
-  } 
-  else {
+  else
     stop("Unknown `acc_pattern`.")
-  }
-
-  invisible(acc_type)
 }
 
+
diff --git a/R/mgfs.R b/R/mgfs.R
index f69dff9..bf78f32 100644
--- a/R/mgfs.R
+++ b/R/mgfs.R
@@ -237,8 +237,7 @@ readMGF <- function (filepath = NULL, filelist = NULL,
   # (2) parallel five MGF files and parallel chunks in each
   len <- length(filelist)
   n_cores <- min(len, detect_cores(32L))
-  # n_cores <- min(detect_cores(32L), floor((find_free_mem()/1024)/(sizes * 8)), len)
-  
+
   if (n_cores == 1L)
     raw_files <- readlineMGFs(1, filelist, filepath, raw_file)
   else {
@@ -323,10 +322,9 @@ readMGF <- function (filepath = NULL, filelist = NULL,
 post_readmgf <- function (df, min_mass = 200L, max_mass = 4500L, ppm_ms1 = 10L, 
                           filepath, out_path) 
 {
-  df <- df %>%
-    dplyr::arrange(ms1_mass) %>%
-    # dplyr::filter(ms1_mass >= min_mass, ms1_mass <= max_mass) %>%
-    dplyr::mutate(frame = find_ms1_interval(ms1_mass, from = min_mass, ppm = ppm_ms1))
+  df <- dplyr::arrange(df, ms1_mass)
+  # df <- dplyr::filter(df, ms1_mass >= min_mass, ms1_mass <= max_mass)
+  df <- dplyr::mutate(df, frame = find_ms1_interval(ms1_mass, from = min_mass, ppm = ppm_ms1))
 
   raws_files <- df$raw_file
   raws <- raws_files[!duplicated.default(raws_files)]
@@ -450,8 +448,6 @@ read_mgf_chunks <- function (filepath = "~/proteoM/mgf/temp_1",
   n_cores <- min(detect_cores(32L), len)
   cl <- parallel::makeCluster(getOption("cl.cores", n_cores))
 
-  parallel::clusterExport(cl, list("%>%"), envir = environment(magrittr::`%>%`))
-  
   parallel::clusterExport(
     cl, 
     c("stri_startswith_fixed", 
@@ -508,7 +504,7 @@ read_mgf_chunks <- function (filepath = "~/proteoM/mgf/temp_1",
                                 digits = digits)
   
   parallel::stopCluster(cl)
-  gc()
+  # gc()
 
   out <- dplyr::bind_rows(out)
 
@@ -536,9 +532,10 @@ read_mgf_chunks <- function (filepath = "~/proteoM/mgf/temp_1",
     
     # perfect case of no gaps: two lines of "" and ""
     if (length(ab) > 2L) ab else NULL
-  }) %>%
-    unlist(use.names = FALSE) %T>%
-    write(file.path(filepath, "gaps.mgf"))
+  })
+  
+  gaps <- unlist(gaps, use.names = FALSE)
+  write(gaps, file.path(filepath, "gaps.mgf"))
 
   local({
     nms <- list.files(path = file.path(filepath), pattern = "^.*\\_[ab]f.mgf$")
@@ -620,11 +617,10 @@ proc_mgf_chunks <- function (file, topn_ms2ions = 100L,
 {
   message("Parsing '", file, "'.")
   lines <- stringi::stri_read_lines(file)
-
   basename <- gsub("\\.[^.]*$", "", file)
-
-  begins <- which(stringi::stri_startswith_fixed(lines, "BEGIN IONS"))
-  ends <- which(stringi::stri_endswith_fixed(lines, "END IONS"))
+  
+  begins <- .Internal(which(stringi::stri_startswith_fixed(lines, "BEGIN IONS")))
+  ends   <- .Internal(which(stringi::stri_endswith_fixed(lines, "END IONS")))
 
   af <- local({
     le <- ends[length(ends)]
@@ -708,8 +704,8 @@ proc_mgfs <- function (lines, topn_ms2ions = 100L,
 {
   options(digits = 9L)
 
-  begins <- which(stringi::stri_startswith_fixed(lines, "BEGIN IONS"))
-  ends <- which(stringi::stri_endswith_fixed(lines, "END IONS"))
+  begins <- .Internal(which(stringi::stri_startswith_fixed(lines, "BEGIN IONS")))
+  ends <- .Internal(which(stringi::stri_endswith_fixed(lines, "END IONS")))
 
   ## MS1 
   # (1) m-over-z and intensity
@@ -751,7 +747,7 @@ proc_mgfs <- function (lines, topn_ms2ions = 100L,
              !is.na(ms1_masses))
   
   # timsTOF data may have undetermined charge states
-  na_rows <- which(is.na(rows))
+  na_rows <- .Internal(which(is.na(rows)))
   if (length(na_rows)) rows[na_rows] <- FALSE
 
   begins <- begins[rows]
@@ -1452,7 +1448,7 @@ read_mzml <- function (xml_file, tmt_reporter_lower = 126.1, tmt_reporter_upper
   ## spectrum
   xml_root <- xml2::read_xml(xml_file)
   mzML <- xml2::xml_child(xml_root)
-  idx_run <- which(xml2::xml_name(xml2::xml_children(mzML)) == "run") # 8
+  idx_run <- which(xml2::xml_name(xml2::xml_children(mzML)) == "run")
   run <- xml2::xml_children(mzML)[[idx_run]]
   idx_specs <- which(xml2::xml_name(xml2::xml_children(run)) == "spectrumList")
   spec <- xml2::xml_children(xml2::xml_children(run)[[idx_specs]])
@@ -1468,14 +1464,14 @@ read_mzml <- function (xml_file, tmt_reporter_lower = 126.1, tmt_reporter_upper
     x <- spec[[i]]
     scan_nums[i] <- gsub(".* scan=(.*)$", "\\1", xml2::xml_attr(x, "id"))
     xc <- xml2::xml_children(x)
-    idx_precursor <- grep("precursorList", xc) # 12
+    idx_precursor <- grep("precursorList", xc)
     rm(list = c("x"))
     
     if (length(idx_precursor)) {
       nms <- xml2::xml_attr(xc, "name")
-      idx_title <- which(nms == "spectrum title") # 10
+      idx_title <- .Internal(which(nms == "spectrum title"))
       idx_scanList <- grep("scanList", xc) # 11
-      idx_bin <- grep("binaryDataArrayList", xc) # 13
+      idx_bin <- grep("binaryDataArrayList", xc)
       
       ## title
       title <- xml2::xml_attr(xc[[idx_title]], "value")
@@ -1486,7 +1482,8 @@ read_mzml <- function (xml_file, tmt_reporter_lower = 126.1, tmt_reporter_upper
       scanList <- xml2::xml_children(xc[[idx_scanList]])
       idx_rt <- grep("scan", scanList) # 2
       scanList_scan <- xml2::xml_children(scanList[[idx_rt]])
-      idx_scan_start <- which(xml2::xml_attr(scanList_scan, "name") == "scan start time") # 1
+      idx_scan_start <- 
+        .Internal(which(xml2::xml_attr(scanList_scan, "name") == "scan start time"))
       ret_times[i] <- xml2::xml_attr(scanList_scan[[idx_scan_start]], "value")
       rm(list = c("nms", "title", "scanList_scan", "scanList"))
       
diff --git a/R/ms1_precursors.R b/R/ms1_precursors.R
index 17f06a6..48b1661 100644
--- a/R/ms1_precursors.R
+++ b/R/ms1_precursors.R
@@ -549,11 +549,12 @@ calc_pepmasses2 <- function (aa_masses = NULL,
             min_mass = min_mass, 
             max_mass = max_mass, 
             digits = digits
-          ) %>% 
-            flatten_list() %>% 
-            unlist(recursive = FALSE, use.names = TRUE)
-
+          )
+          
           parallel::stopCluster(cl)
+          
+          fwd_peps[[i]] <- flatten_list(fwd_peps[[i]])
+          fwd_peps[[i]] <- unlist(fwd_peps[[i]], recursive = FALSE, use.names = TRUE)
           gc()
         }
       }
@@ -591,6 +592,18 @@ calc_pepmasses2 <- function (aa_masses = NULL,
                                "amods+ tmod+ vnl+ fnl+"))
 
     if (length(inds)) {
+      cl <- parallel::makeCluster(getOption("cl.cores", n_cores))
+      
+      parallel::clusterExport(
+        cl,
+        c("hms1_a1_vnl0_fnl0", 
+          "ms1_a1_vnl0_fnl0", 
+          "match_mvmods", 
+          "expand_grid_rows", 
+          "recur_flatten", 
+          "delta_ms1_a0_fnl1"), 
+        envir = environment(proteoM:::ms1_a1_vnl0_fnl0))
+
       for (i in inds) {
         amods_i <- amods[[i]]
         aa_masses_i <- aa_masses_all[[i]]
@@ -610,19 +623,7 @@ calc_pepmasses2 <- function (aa_masses = NULL,
 
         vmods_nl_i = vmods_nl[[i]]
         fmods_nl_i = fmods_nl[[i]]
-        
-        cl <- parallel::makeCluster(getOption("cl.cores", n_cores))
-        
-        parallel::clusterExport(
-          cl,
-          c("hms1_a1_vnl0_fnl0", 
-            "ms1_a1_vnl0_fnl0", 
-            "match_mvmods", 
-            "expand_grid_rows", 
-            "recur_flatten", 
-            "delta_ms1_a0_fnl1"), 
-          envir = environment(proteoM:::ms1_a1_vnl0_fnl0))
-        
+
         fwd_peps[[i]] <- parallel::clusterApply(
           cl, 
           chunksplit(fwd_peps_i, n_cores, "list"), 
@@ -636,19 +637,19 @@ calc_pepmasses2 <- function (aa_masses = NULL,
           ms1vmods = ms1vmods_i, 
           min_mass = min_mass, 
           max_mass = max_mass, 
-          digits = digits
-        ) %>% 
-          flatten_list() %>% 
-          unlist(recursive = FALSE, use.names = TRUE)
-
-        parallel::stopCluster(cl)
-        gc()
+          digits = digits)
+        
+        fwd_peps[[i]] <- flatten_list(fwd_peps[[i]])
+        fwd_peps[[i]] <- unlist(fwd_peps[[i]], recursive = FALSE, use.names = TRUE)
 
         message("\tCompleted peptide masses: ",
                 paste(attributes(aa_masses_i)$fmods, "|", 
                       attributes(aa_masses_i)$vmods,
                       collapse = ", "))
       }
+      
+      parallel::stopCluster(cl)
+      gc()
     }
 
     suppressWarnings(
@@ -1062,6 +1063,15 @@ calc_aamasses <- function (fixedmods = c("TMT6plex (K)",
     save_mod_indexes(out_path, fixedmods, varmods, f_to_v)
     qs::qsave(aa_masses_ms1, file.path(out_path, "aa_masses_ms1.rds"), preset = "fast")
     qs::qsave(aa_masses_all, file.path(out_path, "aa_masses_all.rds"), preset = "fast")
+    
+    fmods <- lapply(aa_masses_all, attr, "fmods", exact = TRUE)
+    vmods <- lapply(aa_masses_all, attr, "vmods", exact = TRUE)
+    
+    readr::write_tsv(
+      data.frame(pep_fmod = unlist(fmods, recursive = FALSE), 
+                 pep_vmod = unlist(vmods, recursive = FALSE), 
+                 pep_mod_group = seq_along(aa_masses_all)), 
+      file.path(out_path, "summary_mod_groups.txt"))
   }
   
   invisible(aa_masses_all)
@@ -1119,10 +1129,10 @@ save_mod_indexes <- function (out_path = NULL, fixedmods, varmods, f_to_v)
   if (is.null(out_path))
     return(NULL)
   
-  mod_indexes <- seq_along(c(fixedmods, varmods)) %>%
-    as.hexmode() %>%
-    `names<-`(c(fixedmods, varmods))
-  
+  mod_indexes <- seq_along(c(fixedmods, varmods))
+  mod_indexes <- as.hexmode(mod_indexes)
+  names(mod_indexes) <- c(fixedmods, varmods)
+
   is_coerced <- if (length(f_to_v)) 
     names(mod_indexes) %in% f_to_v
   else 
@@ -1253,12 +1263,13 @@ find_f_to_v <- function (fixedmods, fmods_ps, vmods_ps)
   
   # e.g. "N-term" can be matched by both site and position
   # (no guarantee in the order of coerce_sites; so match names one at a time)
-  coerce_sites <- unique(c(coerce_asites, coerce_tsites)) %>% 
-    lapply(function (x) {
-      names(x) <- fixedmods[fmods_ps == x]
-      x
-    })
+  coerce_sites <- unique(c(coerce_asites, coerce_tsites))
   
+  coerce_sites <- lapply(coerce_sites, function (x) {
+    names(x) <- fixedmods[fmods_ps == x]
+    x
+  })
+
   unlist(coerce_sites)
 }
 
@@ -1292,9 +1303,9 @@ find_aamasses_vmodscombi <- function (varmods = NULL, f_to_v = NULL,
   varmods_comb <- unlist(varmods_comb, recursive = FALSE)
   vmods_ps <- find_modps(varmods)
 
-  vmods_ps_combi <- seq_along(vmods_ps) %>%
-    lapply(function (x) sim_combn(vmods_ps, x)) %>%
-    flatten_list()
+  vmods_ps_combi <- seq_along(vmods_ps)
+  vmods_ps_combi <- lapply(vmods_ps_combi, function (x) sim_combn(vmods_ps, x))
+  vmods_ps_combi <- flatten_list(vmods_ps_combi)
 
   ## Remove the combinations without anywhere_coerce_sites
   # [x] e.g. "TMT6plex (K)" coerced from fixedmod to varmod, 
@@ -1598,9 +1609,9 @@ check_resunimod <- function (res)
 check_fmods_pos_site <- function (positions_sites)
 {
   if (length(positions_sites) > 1L) {
-    dups <- purrr::reduce(positions_sites, `c`) %>%
-      .[duplicated(.)]
-    
+    dups <- purrr::reduce(positions_sites, `c`)
+    dups <- dups[duplicated(dups)]
+
     if (length(dups)) {
       dups_in_each <- lapply(positions_sites, function (x) x == dups)
       dup_mods <- names(positions_sites[unlist(dups_in_each)])
diff --git a/R/ms2_a1_vnl1_fnl0.R b/R/ms2_a1_vnl1_fnl0.R
index 2c4ea82..8ba4b71 100644
--- a/R/ms2_a1_vnl1_fnl0.R
+++ b/R/ms2_a1_vnl1_fnl0.R
@@ -277,7 +277,7 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
   aam <- aa_masses[aas]
   
   ms1vmods <- match_mvmods(aas = aas, ms1vmods = ms1vmods, amods = amods)
-  oks <- ms1vmods$inds
+  oks <- ms1vmods[["inds"]]
   ms2vmods <- ms2vmods[oks]
   
   vmods_combi <- find_vmodscombi(aas = aas, ms2vmods = ms2vmods, 
@@ -295,20 +295,11 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
     return(NULL)
   
   vnl_combi <- lapply(vmods_combi, function (x) expand_grid_rows(vmods_nl[x]))
+  
   vnl_combi <- lapply(vnl_combi, function (x) 
     if (length(x) > maxn_vnl_per_seq) x[1:maxn_vnl_per_seq] else x)
 
-  ## --- (tentative) to restricts the total number of vnl_combi's
-  # nrows <- lapply(vnl_combi, function (x) length(attributes(x)$row.names)) # faster than nrow
-  # nrows <- .Internal(unlist(nrows, recursive = FALSE, use.names = FALSE))
-  # counts <- cumsum(nrows)
-  
-  # oks <- which(counts <= maxn_vmods_sitescombi_per_pep)
-  # vnl_combi <- vnl_combi[oks]
-  # vmods_combi <- vmods_combi[oks]
-  ## ---
-  
-  # 725 us
+  # theoretical MS2 of forward sequences
   af <- mapply(
     calc_ms2ions_a1_vnl1_fnl0, 
     vmods_combi = vmods_combi, 
@@ -324,15 +315,12 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
     SIMPLIFY = FALSE, 
     USE.NAMES = FALSE)
   
-  # 360 us
-  len <- length(aas)
-  
   af <- mapply(
     add_hexcodes_vnl2, 
     ms2ions = af, 
     vmods_combi = vmods_combi, 
     MoreArgs = list(
-      len = len, 
+      len = length(aas), 
       mod_indexes  = mod_indexes), 
     SIMPLIFY = FALSE, 
     USE.NAMES = FALSE)
@@ -342,8 +330,9 @@ gen_ms2ions_a1_vnl1_fnl0 <- function (aa_seq = NULL, ms1_mass = NULL,
   if (length(af) > maxn_vmods_sitescombi_per_pep) 
     af <- af[1:maxn_vmods_sitescombi_per_pep]
   
-  # need to fix hex tags which will not be used; 
-  # for time efficiency just leave as
+  # hexcodes of the reversed entries are not yet reversed; 
+  #  they are not used and for time efficiency just leave them as are
+  # names are `pep_ivmod`; NA is the indicator for reversed entries
   av <- lapply(af, calc_rev_ms2, aas)
   names(av) <- NA_character_
   c(af, av)
@@ -366,25 +355,30 @@ calc_ms2ions_a1_vnl1_fnl0 <- function (vmods_combi, vnl_combi, aam, aa_masses,
 {
   # updates vmod masses
   delta_amod <- aa_masses[vmods_combi]
-  idxes <- as.numeric(names(vmods_combi))
+  idxes <- as.integer(names(vmods_combi))
   aam[idxes] <- aam[idxes] + delta_amod
   
   # updates vnl masses
   len <- length(vnl_combi)
   out <- vector("list", len)
   
-  for (i in 1:len) {
-    aam_i <- aam
-    delta_nl <- .Internal(unlist(vnl_combi[[i]], recursive = FALSE, use.names = FALSE))
-    aam_i[idxes] <- aam_i[idxes] - delta_nl
-    out[[i]] <- ms2ions_by_type(aam_i, ntmass, ctmass, type_ms2ions, digits)
+  # the first vnl masses are always all zeros
+  out[[1]] <- ms2ions_by_type(aam, ntmass, ctmass, type_ms2ions, digits)
+  
+  if (len > 1L) {
+    for (i in 2:len) {
+      aam_i <- aam
+      delta_nl <- .Internal(unlist(vnl_combi[[i]], recursive = FALSE, use.names = FALSE))
+      aam_i[idxes] <- aam_i[idxes] - delta_nl
+      out[[i]] <- ms2ions_by_type(aam_i, ntmass, ctmass, type_ms2ions, digits)
+    }
   }
 
   invisible(out)
 }
 
 
-#' Adds hex codes (with variable NLs).
+#' Adds hexcodes (with variable NLs).
 #' 
 #' To indicate the variable modifications of an amino acid sequence.
 #' 
@@ -393,11 +387,9 @@ calc_ms2ions_a1_vnl1_fnl0 <- function (vmods_combi, vnl_combi, aam, aa_masses,
 #' @inheritParams ms2match
 add_hexcodes_vnl2 <- function (ms2ions, vmods_combi, len, mod_indexes = NULL) 
 {
-  # idxes <- .Internal(unlist(vmods_combi, recursive = FALSE, use.names = FALSE))
   nms <- names(vmods_combi)
   
   hexs <- rep("0", len)
-  # hexs[as.integer(nms)] <- mod_indexes[idxes]
   hexs[as.integer(nms)] <- mod_indexes[vmods_combi]
   hexs <- .Internal(paste0(list(hexs), collapse = "", recycle0 = FALSE))
 
diff --git a/R/ms2_base.R b/R/ms2_base.R
index 04505cf..1895293 100644
--- a/R/ms2_base.R
+++ b/R/ms2_base.R
@@ -870,7 +870,7 @@ find_ms2_bypep <- function (theos = NULL, expts = NULL, ex = NULL, d = NULL,
     
     ## forward matches
     ps <- th_i %fin% ex | (th_i - 1L) %fin% ex | (th_i + 1L) %fin% ex
-    ips <- which(ps)
+    ips <- .Internal(which(ps))
     
     ## "ith = ips" in ascending order, not "iex = ips_12"
 
@@ -894,12 +894,12 @@ find_ms2_bypep <- function (theos = NULL, expts = NULL, ex = NULL, d = NULL,
       # b-ions
       y_1 <- th_i[1:mid]
       ps_1 <- ex %fin% y_1 | ex_bf %fin% y_1 | ex_af %fin% y_1
-      ips_1 <- which(ps_1) 
-      
+      ips_1 <- .Internal(which(ps_1))
+
       # y-ions
       y_2 <- th_i[(mid+1L):lth]
       ps_2 <- ex %fin% y_2 | ex_bf %fin% y_2 | ex_af %fin% y_2
-      ips_2 <- which(ps_2) 
+      ips_2 <- .Internal(which(ps_2))
       
       # b- and y-ions
       expt_1 <- expts[ips_1]
diff --git a/R/msmsmatches.R b/R/msmsmatches.R
index 6879295..e33c875 100644
--- a/R/msmsmatches.R
+++ b/R/msmsmatches.R
@@ -269,7 +269,7 @@
 #' @param fdr_type A character string; the type of FDR control. The value is in
 #'   one of c("protein", "peptide", "psm"). The default is \code{protein}.
 #'
-#'   Note that \code{fdr_type = protein} is equivalent to \code{fdr_type =
+#'   Note that \code{fdr_type = protein} is comparable to \code{fdr_type =
 #'   peptide} with the additional filtration of data at \code{prot_tier == 1}.
 #' @param fdr_group A character string; the modification group(s) for uses in
 #'   peptide FDR controls. The value is in one of c("all", "base"). The
@@ -277,8 +277,7 @@
 #'   of matches.
 #' @param max_pepscores_co A positive numeric; the upper limit in the cut-offs
 #'   of peptide scores for discriminating significant and insignificant
-#'   identities. The default is changed from \code{Inf} to 50 from version
-#'   1.1.9.2 on.
+#'   identities.
 #' @param min_pepscores_co A non-negative numeric; the lower limit in the
 #'   cut-offs of peptide scores for discriminating significant and insignificant
 #'   identities.
@@ -300,10 +299,10 @@
 #'   pep_score_cutoff} under a protein will be used to represent the threshold
 #'   of a protein enrichment score. For more conserved thresholds, the
 #'   statistics of \code{"max"} may be considered.
-#' @param soft_secions Logical; if TRUE, collapses the intensities of secondary
-#'   ions to primary ions at the absence of the primaries. The default is FALSE.
-#'   For instance, the signal of \code{b5^*} will be ignored if its primary ion
-#'   \code{b5} is not matched.
+#' @param soft_secions Depreciated. Logical; if TRUE, collapses the intensities
+#'   of secondary ions to primary ions at the absence of the primaries. The
+#'   default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+#'   if its primary ion \code{b5} is not matched.
 #' @param topn_seqs_per_query Positive integer; a threshold to discard peptide
 #'   matches under the same MS query with scores beyond the top-n.
 #'
@@ -319,17 +318,20 @@
 #'
 #'   For a variable modification with multiple neutral losses (NL), the
 #'   best-scored NL will be used in the ranking.
-#' @param combine_tier_three Logical; if TRUE, combines search results at tiers
-#'   1, 2 and 3 to the single output of \code{psmQ.txt}. The default is FALSE in
-#'   that data will be segregated into the three quality tiers according to the
-#'   choice of \code{fdr_type}. The (convenience) parameter matters since
-#'   \href{http://github.com/qzhang503/proteoQ}{proteoQ} will only look for the
-#'   inputs of \code{psmQ[...].txt}.
-#'
-#'   For instance, if the aim is to bypass the constraint by protein FDR and
-#'   focus on PSMs that have met the cut-offs specified by \code{target_fdr}, an
-#'   experimenter may set \code{combine_tier_three = TRUE} and hence pool all
-#'   significant peptides in \code{psmQ.txt} for downstream proteoQ.
+#' @param combine_tier_three Logical; if TRUE, combines search results at tier-3
+#'   to tier-1 to form the single output of \code{psmQ.txt}. The default is
+#'   FALSE in that data will be segregated into the three quality tiers (shown
+#'   below) by the choice of \code{fdr_type}. Note that the argument affects
+#'   only at the \code{fdr_type} of \code{psm} or \code{peptide} where there are
+#'   no tier-2 outputs. In general, the tier-3 results correspond to
+#'   one-hit-wonders and setting \code{combine_tier_three = TRUE} is
+#'   discouraged.
+#'
+#'   In subproteome analysis, such as phosphoproteome analysis, some proteins
+#'   may be well established globally, but fail the significance assessment by
+#'   protein FDR on the local scale. In situations like this, it may be suitable
+#'   to apply \code{fdr_type = "peptide"} or \code{fdr_type = "psm"} other than
+#'   incurring \code{combine_tier_three = TRUE}.
 #'
 #'   Tier-1: both proteins and peptides with scores above significance
 #'   thresholds.
@@ -382,9 +384,6 @@
 #'   file folder for disk space or under infrequent events of modified framework
 #'   incurred by the developer.
 #'
-#'   Started from version 1.2.1.5, a new data structure of protein-peptide
-#'   lookups are used. Version 1.2.1.4.1 is the final version using the old data
-#'   structure.
 #' @param .path_fasta The parent file path to the theoretical masses of MS1
 #'   precursors. At the NULL default, the path is \code{gsub("(.*)\\.[^\\.]*$",
 #'   "\\1", get("fasta", envir = environment())[1])}. The parameter is for the
@@ -634,17 +633,19 @@ matchMS <- function (out_path = "~/proteoM/outs",
                                 "SemiGluN", "SemiAspC", "SemiAspN", "Noenzyme", 
                                 "Nodigest"),
                      custom_enzyme = c(Cterm = NULL, Nterm = NULL), 
-                     nes_fdr_group = c("all", "all_cterm_tryptic", 
-                                       "all_cterm_nontryptic", "base", 
-                                       "base_cterm_tryptic", 
-                                       "base_cterm_nontryptic"), 
+                     nes_fdr_group = c("base", "base_cterm_tryptic", 
+                                       "base_cterm_nontryptic", 
+                                       "all", "all_cterm_tryptic", 
+                                       "all_cterm_nontryptic", 
+                                       "top3", "top3_cterm_tryptic", 
+                                       "top3_cterm_nontryptic"), 
                      noenzyme_maxn = 0L, 
                      maxn_fasta_seqs = 200000L,
                      maxn_vmods_setscombi = 512L,
                      maxn_vmods_per_pep = 5L,
                      maxn_sites_per_vmod = 3L,
-                     maxn_fnl_per_seq = 64L, 
-                     maxn_vnl_per_seq = 64L, 
+                     maxn_fnl_per_seq = 8L, 
+                     maxn_vnl_per_seq = 8L, 
                      maxn_vmods_sitescombi_per_pep = 64L,
                      min_len = 7L, max_len = 40L, max_miss = 2L, 
                      min_mass = 200L, max_mass = 4500L, 
@@ -669,7 +670,7 @@ matchMS <- function (out_path = "~/proteoM/outs",
                      
                      target_fdr = 0.01,
                      fdr_type = c("protein", "peptide", "psm"),
-                     fdr_group = c("all", "base"), 
+                     fdr_group = c("base", "all", "top3"), 
                      max_pepscores_co = 50, min_pepscores_co = 0, 
                      max_protscores_co = Inf, 
                      max_protnpep_co = 10L, 
@@ -931,10 +932,13 @@ matchMS <- function (out_path = "~/proteoM/outs",
   }
   
   # fdr_group
+  
+  # for future supports of character strings or integers (mod_groups)
+  # fdr_group <- check_fdr_group(fdr_group, eval(this_fml[["fdr_group"]]))
   oks <- eval(this_fml[["fdr_group"]])
   fdr_group <- substitute(fdr_group)
   
-  if (length(fdr_group) > 1L)
+  if (length(fdr_group) > 1L && identical(eval(fdr_group), oks))
     fdr_group <- oks[1]
   else {
     fdr_group <- as.character(fdr_group) 
@@ -942,12 +946,12 @@ matchMS <- function (out_path = "~/proteoM/outs",
     if (!fdr_group %in% oks)
       stop("Incorrect `fdr_group`.")
   }
-  
+
   # nes_fdr_group
   oks <- eval(this_fml[["nes_fdr_group"]])
   nes_fdr_group <- substitute(nes_fdr_group)
   
-  if (length(nes_fdr_group) > 1L)
+  if (length(nes_fdr_group) > 1L && identical(eval(nes_fdr_group), oks))
     nes_fdr_group <- oks[1]
   else {
     nes_fdr_group <- as.character(nes_fdr_group) 
@@ -1284,7 +1288,7 @@ matchMS <- function (out_path = "~/proteoM/outs",
     calc_pepscores(topn_ms2ions = topn_ms2ions,
                    type_ms2ions = type_ms2ions,
                    target_fdr = target_fdr,
-                   fdr_type = fdr_type,
+                   # fdr_type = fdr_type, # not used
                    min_len = min_len,
                    max_len = max_len,
                    ppm_ms2 = ppm_ms2,
@@ -1449,7 +1453,7 @@ matchMS <- function (out_path = "~/proteoM/outs",
 
   df <- try_psmC2Q(df, 
                    out_path = out_path,
-                   fdr_type = fdr_type, 
+                   fdr_type = fdr_type, # for workflow controls 
                    combine_tier_three = combine_tier_three, 
                    max_n_prots = max_n_prots)
   
@@ -1587,6 +1591,7 @@ reproc_psmC <- function (out_path = NULL, fdr_type = "protein",
 #' @param fct A factor for data splitting into chunks. May consider a greater
 #'   value for a larger data set.
 #' @inheritParams matchMS
+#' @importFrom fastmatch %fin%
 psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
                     combine_tier_three = FALSE, max_n_prots = 60000L, 
                     fct = 4L) 
@@ -1595,7 +1600,7 @@ psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
   
   # if (!all(df[["pep_issig"]])) stop("Developer: filter data by \"pep_issig\" first.")
   # if (any(df[["pep_isdecoy"]])) stop("Developer: remove decoy peptide first.")
-  # if (any(grepl("^-", df["prot_acc"]))) stop("Developr: remove decoy proteins first.")
+  # if (any(grepl("^-", df["prot_acc"]))) stop("Developer: remove decoy proteins first.")
 
   message("\n=================================\n",
           "prot_tier  prot_issig  prot_n_pep \n",
@@ -1605,26 +1610,22 @@ psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
           "=================================\n")
   
   # Set aside one-hit wonders
-  df3 <- df %>%
-    dplyr::filter(!prot_issig, prot_n_pep == 1L) %>%
-    dplyr::mutate(prot_tier = 3L)
-  
+  df3 <- dplyr::filter(df, !prot_issig, prot_n_pep == 1L)
+  df3 <- dplyr::mutate(df3, prot_tier = 3L)
+
   df <- dplyr::bind_rows(
     dplyr::filter(df, prot_issig),
-    dplyr::filter(df, !prot_issig, prot_n_pep >= 2L)
-  ) %>%
-    dplyr::mutate(prot_tier = ifelse(prot_issig, 1L, 2L))
-  
+    dplyr::filter(df, !prot_issig, prot_n_pep >= 2L))
+
+  df <- dplyr::mutate(df, prot_tier = ifelse(prot_issig, 1L, 2L))
+
   # the same peptide can be present in all three protein tiers; 
   # steps up if pep_seq(s) in tier 3 also in tiers 1, 2
   if (FALSE) {
     rows <- df3$pep_seq %in% df$pep_seq
-    
     df <- dplyr::bind_rows(df, df3[rows, ])
     df3 <- df3[!rows, ]
-    
     rm(list = "rows")
-    gc()
   }
   
   # Protein groups
@@ -1641,12 +1642,12 @@ psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
     fdr_type <- "protein"
     
     df2 <- dplyr::filter(df, prot_tier == 2L)
-    df <- dplyr::filter(df, prot_tier == 1L)
+    df  <- dplyr::filter(df, prot_tier == 1L)
   } 
   else {
     if (fdr_type == "protein") {
       df2 <- dplyr::filter(df, prot_tier == 2L)
-      df <- dplyr::filter(df, prot_tier == 1L)
+      df  <- dplyr::filter(df, prot_tier == 1L)
     } 
     else {
       message("No tier-2 outputs at `fdr_type = ", fdr_type, "`.")
@@ -1665,7 +1666,7 @@ psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
   # df may have both prot_tier 1 and 2 if fdr_type != "protein"
   df_tier12 <- unique(df[, c("prot_acc", "prot_tier")])
   
-  df <- unique(df[, c("prot_acc", "pep_seq")])
+  df  <- unique(df [, c("prot_acc", "pep_seq")])
   df2 <- unique(df2[, c("prot_acc", "pep_seq")])
   df3 <- unique(df3[, c("prot_acc", "pep_seq")])
   gc()
@@ -1680,26 +1681,25 @@ psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
   else
     df <- make_zero_df(nms)
 
-  if (nrow(df2)) 
-    df2 <- groupProts(df2, out_path = file.path(out_path, "temp2"), fct = fct)
+  df2 <- if (nrow(df2)) 
+    groupProts(df2, out_path = file.path(out_path, "temp2"), fct = fct)
   else 
-    df2 <- make_zero_df(nms)
+    make_zero_df(nms)
   
-  if (nrow(df3)) 
-    df3 <- groupProts(df3, out_path = file.path(out_path, "temp3"), fct = fct)
+  df3 <- if (nrow(df3)) 
+    groupProts(df3, out_path = file.path(out_path, "temp3"), fct = fct)
   else 
-    df3 <- make_zero_df(nms)
+    make_zero_df(nms)
   
   rm(list = c("nms", "df_tier12"))
 
   # Cleanup
   dfC <- suppressWarnings(
-    read_tsv(file.path(out_path, "psmC.txt"), col_types = get_proteoM_coltypes())
-  ) %>% 
-    dplyr::filter(pep_issig, !pep_isdecoy, !grepl("^-", prot_acc)) %>% 
-    tidyr::unite(uniq_id, prot_acc, pep_seq, sep = ".", remove = FALSE)
-  
-  df <- post_psmC2Q(df, dfC, tier = NULL)
+    read_tsv(file.path(out_path, "psmC.txt"), col_types = get_proteoM_coltypes()))
+  dfC <- dplyr::filter(dfC, pep_issig, !pep_isdecoy, !grepl("^-", prot_acc))
+  dfC <- tidyr::unite(dfC, uniq_id, prot_acc, pep_seq, sep = ".", remove = FALSE)
+
+  df  <- post_psmC2Q(df,  dfC, tier = NULL)
   df2 <- post_psmC2Q(df2, dfC, tier = 2L)
   df3 <- post_psmC2Q(df3, dfC, tier = 3L)
   
@@ -1721,11 +1721,11 @@ psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
   }
   
   if (combine_tier_three) {
-    df <- list(df, df2, df3) %>%
-      dplyr::bind_rows() %>%
-      dplyr::arrange(prot_acc, pep_seq) %T>%
-      readr::write_tsv(file.path(out_path, "psmQ.txt"))
-    
+    df3 <- df3[!df3[["pep_seq"]] %fin% df[["pep_seq"]], ]
+    df <- dplyr::bind_rows(list(df, df3)) # df2 should have no rows
+    df <- dplyr::arrange(df, prot_acc, pep_seq)
+    readr::write_tsv(df, file.path(out_path, "psmQ.txt"))
+
     local({
       file_t2 <- file.path(out_path, "psmT2.txt")
       file_t3 <- file.path(out_path, "psmT3.txt")
@@ -1742,22 +1742,18 @@ psmC2Q <- function (df = NULL, out_path = NULL, fdr_type = "protein",
     })
   } 
   else {
-    df <- df %>%
-      dplyr::arrange(prot_acc, pep_seq) %T>%
-      readr::write_tsv(file.path(out_path, "psmQ.txt"))
-    
+    df <- dplyr::arrange(df, prot_acc, pep_seq)
+    readr::write_tsv(df, file.path(out_path, "psmQ.txt"))
+
     if (nrow(df2)) {
-      df2 <- df2[names(df)] %>%
-        dplyr::mutate(prot_hit_num = prot_hit_num + max)  %T>%
-        readr::write_tsv(file.path(out_path, "psmT2.txt"))
-      
-      max <- max(df2$prot_hit_num, na.rm = TRUE)
+      df2 <- dplyr::mutate(df2[names(df)], prot_hit_num = prot_hit_num + max)
+      readr::write_tsv(df2, file.path(out_path, "psmT2.txt"))
+      max <- max(df2[["prot_hit_num"]], na.rm = TRUE)
     }
     
     if (nrow(df3)) {
-      df3 <- df3[names(df)] %>%
-        dplyr::mutate(prot_hit_num = prot_hit_num + max)  %T>%
-        readr::write_tsv(file.path(out_path, "psmT3.txt"))
+      df3 <- dplyr::mutate(df3[names(df)], prot_hit_num = prot_hit_num + max)
+      readr::write_tsv(df3, file.path(out_path, "psmT3.txt"))
     }
   }
   
@@ -1776,11 +1772,10 @@ post_psmC2Q <- function (df, dfC, tier = NULL)
   if (!is.null(tier))
     df <- dplyr::mutate(df, prot_tier = tier)
 
-  df <- df %>% 
-    tidyr::unite(uniq_id, prot_acc, pep_seq, sep = ".", remove = TRUE) %>% 
-    dplyr::left_join(dfC, by = "uniq_id") %>% 
-    dplyr::select(-uniq_id)
-  
+  df <- tidyr::unite(df, uniq_id, prot_acc, pep_seq, sep = ".", remove = TRUE)
+  df <- dplyr::left_join(df, dfC, by = "uniq_id")
+  df <- dplyr::select(df, -uniq_id)
+
   ord_prots <- c("prot_acc", "prot_issig")
   
   df <- dplyr::bind_cols(
@@ -1797,14 +1792,13 @@ post_psmC2Q <- function (df, dfC, tier = NULL)
   )
   
   df <- dplyr::bind_cols(
-    df %>% .[grepl("^prot_", names(.))],
-    df %>% .[grepl("^pep_", names(.))],
-    df %>% .[grepl("^psm_", names(.))],
-    df %>% .[!grepl("^prot_|^pep_|^psm_", names(.))],
+    df[grepl("^prot_", names(df))],
+    df[grepl("^pep_", names(df))],
+    df[grepl("^psm_", names(df))],
+    df[!grepl("^prot_|^pep_|^psm_", names(df))],
   )
   
-  df <- df %>% 
-    dplyr::select(-which(names(.) %in% c("prot_n_psm", "prot_n_pep")))
+  df <- dplyr::select(df, -which(names(df) %in% c("prot_n_psm", "prot_n_pep")))
 }
 
 
@@ -1992,3 +1986,32 @@ map_raw_n_scan <- function (df, mgf_path)
 }
 
 
+#' Checks the values of \code{fdr_group}
+#' 
+#' Not yet used. Takes values of integers or character strings.
+#' 
+#' @inheritParams matchMS
+check_fdr_group <- function (fdr_group = c("base", "all", "top3"), 
+                             oks = c("base", "all"))
+{
+  is_trivial <- all(is.null(fdr_group)) || all(is.na(fdr_group)) || 
+    all(fdr_group == "")
+  
+  if (is_trivial)
+    return(oks[[1]])
+  
+  fdr_group <- unique(fdr_group)
+  
+  len <- length(fdr_group)
+  
+  if (len > 1L) {
+    if (all(fdr_group %in% oks))
+      fdr_group <- oks[1]
+    else
+      fdr_group <- fdr_group[!fdr_group %in% oks]
+  }
+  
+  as.character(fdr_group)
+}
+
+
diff --git a/R/scores.R b/R/scores.R
index dff320c..1cc2183 100644
--- a/R/scores.R
+++ b/R/scores.R
@@ -266,16 +266,8 @@ calc_probi_byvmods <- function (df, nms, expt_moverzs, expt_ints,
 
   ## df2
   tt2 <- add_seions(df_theo, type_ms2ions = type_ms2ions, digits = digits)
+  df2 <- match_ex2th2(expt_moverzs, tt2, min_ms2mass, d2, index_mgf_ms2)
   
-  if (index_mgf_ms2) {
-    # df2 <- find_ppm_outer_bycombi(expt_moverzs, index_mz(tt2, from = min_ms2mass, d = d2), 2L)
-    df2 <- match_ex2th2(expt_moverzs, tt2, min_ms2mass, d2, index_mgf_ms2)
-  }
-  else {
-    # df2 <- find_ppm_outer_bycombi(expt_moverzs, tt2, ppm_ms2)
-    df2 <- match_ex2th2(expt_moverzs, tt2, min_ms2mass, d2, index_mgf_ms2)
-  }
-
   ith2 <- df2[["ith"]]
   iex2 <- df2[["iex"]]
 
@@ -313,7 +305,7 @@ calc_probi_byvmods <- function (df, nms, expt_moverzs, expt_ints,
   
   ## 3. join `int2` to `y`
   y_idx <- y[["idx"]]
-  ok_iex <- which(!is.na(y_idx))
+  ok_iex <- .Internal(which(!is.na(y_idx)))
   y_ith <- y_idx[ok_iex]
   y[["int2"]][ok_iex] <- int2[y_ith]
   
@@ -323,7 +315,7 @@ calc_probi_byvmods <- function (df, nms, expt_moverzs, expt_ints,
   
   ###
   if (soft_secions) {
-    ok_int2 <- which(int2 > 0L & is.na(df[["int"]])) # 11, 21
+    ok_int2 <- .Internal(which(int2 > 0L & is.na(df[["int"]])))
     
     if (length(ok_int2)) {
       ok_iex2 <- iex2[match(ok_int2, ith2 %% m)]
@@ -337,7 +329,7 @@ calc_probi_byvmods <- function (df, nms, expt_moverzs, expt_ints,
   ## 5. arrange by "-int"
   ord_int <- order(y[["int"]], decreasing = TRUE, method = "radix", na.last = TRUE)
   y_theo <- y[["theo"]][ord_int]
-  maxi <- which(!is.na(y_theo))
+  maxi <- .Internal(which(!is.na(y_theo)))
   maxi <- maxi[length(maxi)]
   y_theo <- y_theo[1:maxi]
 
@@ -527,8 +519,8 @@ scalc_pepprobs <- function (entry, topn_ms2ions = 100L, type_ms2ions = "by",
   #   3  331.   331.
   
   # (flattens by one level as is a list-column)
-  mts <- entry$matches[[1]]
-  
+  mts <- entry[["matches"]][[1]]
+
   # N <- entry$ms2_n[[1]]
   topn_ms2ions <- min(topn_ms2ions, entry$ms2_n[[1]])
   N <- min(topn_ms2ions * 5L, 500L)
@@ -549,7 +541,7 @@ scalc_pepprobs <- function (entry, topn_ms2ions = 100L, type_ms2ions = "by",
   uniq_id <- .Internal(unlist(entry$uniq_id, recursive = FALSE, use.names = FALSE))
   
   out <- lapply(out, function (x) {
-    x$uniq_id <- uniq_id
+    x[["uniq_id"]] <- uniq_id
     x
   })
 
@@ -606,7 +598,11 @@ calc_pepprobs_i <- function (df, topn_ms2ions = 100L, type_ms2ions = "by",
 #' @inheritParams matchMS
 #' @import parallel
 calc_pepscores <- function (topn_ms2ions = 100L, type_ms2ions = "by", 
-                            target_fdr = 0.01, fdr_type = "psm", 
+                            target_fdr = 0.01, 
+                            
+                            # to be deleted later
+                            fdr_type = "protein", 
+                            
                             min_len = 7L, max_len = 40L, ppm_ms2 = 20L, 
                             soft_secions = FALSE, 
                             out_path = "~/proteoM/outs", 
@@ -632,7 +628,7 @@ calc_pepscores <- function (topn_ms2ions = 100L, type_ms2ions = "by",
     add = TRUE
   )
   
-  # Check priors
+  ## Check priors
   pat_i <- "^ion_matches_"
   list_i <- find_targets(out_path, pattern = pat_i)$files
   len_i  <- length(list_i)
@@ -645,10 +641,13 @@ calc_pepscores <- function (topn_ms2ions = 100L, type_ms2ions = "by",
   fun_env <- environment()
   fml_nms <- names(formals(fun))
   
-  # args_except <- c("sys_ram")
-  # fml_incl <- fml_nms[!fml_nms %in% args_except]
-  fml_incl <- fml_nms
+  args_except <- c("fdr_type")
   
+  fml_incl <- if (length(args_except))
+    fml_nms[!fml_nms %in% args_except]
+  else
+    fml_nms
+
   message("[x] For reprocessing (with new score function) ", 
           "delete cached 'pepscores_[...]' and 'calc_pepscores.rda'.\n")
   
@@ -682,14 +681,9 @@ calc_pepscores <- function (topn_ms2ions = 100L, type_ms2ions = "by",
     rm(list = c("cache_pars", "call_pars"))
   }
   
-  # to be deleted
-  # n_cores <- detect_cores(16L)
-  
   d2 <- calc_threeframe_ppm(ppm_ms2) * 1E-6
   
-  for (fi in list_i) {
-    message("\tModule: ", fi)
-    
+  for (fi in list_i)
     calcpepsc(file = fi, 
               topn_ms2ions = topn_ms2ions, 
               type_ms2ions = type_ms2ions, 
@@ -703,18 +697,16 @@ calc_pepscores <- function (topn_ms2ions = 100L, type_ms2ions = "by",
               add_ms2theos2 = add_ms2theos2, 
               add_ms2moverzs = add_ms2moverzs, 
               add_ms2ints = add_ms2ints,
+              # slower with 48 cores
+              n_cores = detect_cores(16L), 
               digits = digits)
-    
-    gc()
-  }
-  
+
   .savecall <- TRUE
   
   invisible(NULL)
 }
 
 
-
 #' Find the index or name of decoy results.
 #' 
 #' @param pattern The pattern of files.
@@ -758,6 +750,7 @@ find_targets <- function (out_path, pattern = "^ion_matches_")
 #' 
 #' @param file A file name of \code{ion_matches_}.
 #' @param d2 Bin width in ppm divided by 1E6.
+#' @param n_cores The number of CPU cores.
 #' @inheritParams matchMS
 #' @inheritParams calc_pepscores
 calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by", 
@@ -765,9 +758,10 @@ calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by",
                        min_ms2mass = 115L, d2 = 1E-5, index_mgf_ms2 = FALSE, 
                        add_ms2theos = FALSE, add_ms2theos2 = FALSE, 
                        add_ms2moverzs = FALSE, add_ms2ints = FALSE, 
-                       digits = 4L) 
+                       n_cores = 16L, digits = 4L) 
 {
-  # (can be decoy => .*, not \\d+)
+  message("\tModule: ", file)
+  
   idx <- gsub("^ion_matches_(.*)\\.rds$", "\\1", file)
   file_lt <- file.path(out_path, "temp", paste0("list_table_", idx, ".rds"))
   file_sc <- file.path(out_path, "temp", paste0("pepscores_", idx, ".rds"))
@@ -820,9 +814,6 @@ calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by",
   #   -> res[[i]] <- NULL 
   #   -> length(res) shortened by 1
   
-  # will be used again later
-  n_cores <- detect_cores(48L)
-  
   if (n_rows <= 5000L) {
     probs <- calc_pepprobs_i(
       df,
@@ -865,9 +856,10 @@ calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by",
       
       for (i in seq_len(len)) {
         dfi <- suppressWarnings(
-          chunksplit(qs::qread(file.path(tempdir, nms[[i]])), n_cores, "row"))
+          # * 4L of smaller hashes for some slow phospho scoring
+          chunksplit(qs::qread(file.path(tempdir, nms[[i]])), n_cores * 4L, "row"))
 
-        probs[[i]] <- parallel::clusterApply(cl, dfi, 
+        probs[[i]] <- parallel::clusterApplyLB(cl, dfi, 
                                              calc_pepprobs_i, 
                                              topn_ms2ions = topn_ms2ions, 
                                              type_ms2ions = type_ms2ions, 
@@ -890,7 +882,7 @@ calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by",
       df <- qs::qread(path_df)
     }
     else {
-      dfs <- suppressWarnings(chunksplit(df, n_cores, "row"))
+      dfs <- suppressWarnings(chunksplit(df, n_cores * 4L, "row"))
       
       # a case that `chunksplit` did not successfully split
       if (is.data.frame(dfs)) {
@@ -907,7 +899,7 @@ calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by",
           digits = digits)
       }
       else {
-        probs <- parallel::clusterApply(cl, dfs, 
+        probs <- parallel::clusterApplyLB(cl, dfs, 
                                         calc_pepprobs_i, 
                                         topn_ms2ions = topn_ms2ions, 
                                         type_ms2ions = type_ms2ions, 
@@ -932,8 +924,6 @@ calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by",
   if ("matches" %in% names(df)) 
     df <- df[, -which(names(df) == "matches"), drop = FALSE]
   
-  gc()
-  
   df2 <- qs::qread(path_df2)
   df <- dplyr::bind_cols(df, df2)
   rm(list = c("df2", "path_df2"))
@@ -946,7 +936,8 @@ calcpepsc <- function (file, topn_ms2ions = 100L, type_ms2ions = "by",
   df <- df[, -which(names(df) == "uniq_id"), drop = FALSE]
   df <- post_pepscores(df)
 
-  ## Outputs 
+  
+  ## Add MS2 m/z and intensity values 
   qs::qsave(df[, cols_lt, drop = FALSE], file_lt, preset = "fast")
   
   message("\tAdding theoretical MS2 m/z and intensity values: ", Sys.time())
@@ -1266,16 +1257,30 @@ find_pepscore_co2 <- function (td, target_fdr = 0.01)
 #' @param td A target-decoy pair.
 #' @param len Numeric; the length of peptides.
 #' @inheritParams matchMS
-probco_bypeplen <- function (len, td, fdr_type = "psm", target_fdr = 0.01, 
+probco_bypeplen <- function (len, td, fdr_type = "protein", target_fdr = 0.01, 
                              min_pepscores_co = 0, out_path) 
 {
   td <- dplyr::filter(td, pep_len == len)
   
   if (fdr_type %in% c("peptide", "protein")) {
-    td <- dplyr::arrange(td, pep_seq, pep_prob)
-    td <- dplyr::group_by(td, pep_seq)
-    td <- dplyr::filter(td, row_number() == 1L)
-    td <- dplyr::ungroup(td)
+    if (fdr_type == "protein") {
+      td <- dplyr::arrange(td, pep_seq, pep_prob)
+      td <- dplyr::group_by(td, pep_seq)
+      td <- dplyr::filter(td, row_number() == 1L)
+      td <- dplyr::ungroup(td)
+    }
+    else {
+      # td[["pep_ivmod2"]] <- gsub(" [\\(\\[]\\d+[\\)\\[]$", "", td[["pep_ivmod"]])
+      td[["pep_ivmod2"]] <- gsub(" .*", "", td[["pep_ivmod"]])
+      td[["pep_seq_mod"]] <- ifelse(is.na(td[["pep_ivmod2"]]), td[["pep_seq"]], 
+                                    paste0(td[["pep_seq"]], ".", td[["pep_ivmod2"]]))
+      td <- dplyr::arrange(td, pep_seq_mod, pep_prob)
+      td <- dplyr::group_by(td, pep_seq_mod)
+      td <- dplyr::filter(td, row_number() == 1L)
+      td <- dplyr::ungroup(td)
+      td[["pep_ivmod2"]] <- NULL
+      td[["pep_seq_mod"]] <- NULL
+    }
   }
 
   td <- dplyr::select(td, pep_prob, pep_isdecoy)
@@ -1288,7 +1293,7 @@ probco_bypeplen <- function (len, td, fdr_type = "psm", target_fdr = 0.01,
   count <- nrow(td)
   
   if (count < (1 / target_fdr)) {
-    if (count <= 20L) 
+    if (count <= 10L) # changed from 20L
       return(NA)
     
     best_co <- tryCatch(
@@ -1508,12 +1513,12 @@ find_probco_valley <- function (prob_cos, guess = 12L)
 #' }
 #' 
 #' }
-calc_pepfdr <- function (target_fdr = .01, fdr_type = "psm", 
+calc_pepfdr <- function (target_fdr = .01, fdr_type = "protein", 
                          min_len = 7L, max_len = 40L, 
                          max_pepscores_co = 50, min_pepscores_co = 0, 
                          enzyme = "trypsin_p", 
-                         fdr_group = "all", 
-                         nes_fdr_group = "all", 
+                         fdr_group = "base", 
+                         nes_fdr_group = "base", 
                          out_path) 
 {
   message("Calculating peptide FDR.")
@@ -1522,7 +1527,12 @@ calc_pepfdr <- function (target_fdr = .01, fdr_type = "psm",
   
   files <- list.files(path = file.path(out_path, "temp"), 
                       pattern = "^pepscores_", full.names = TRUE)
-  max_i <- which.max(file.size(files))[[1]]
+  
+  top3s <- gsub(paste0("^.*pepscores_", "(\\d+)\\.rds$"), "\\1", 
+                files[which_topx2(file.size(files), 3L)[1:3]])
+
+  max_i <- gsub(paste0("^.*pepscores_", "(\\d+)\\.rds$"), "\\1", 
+                files[which.max(file.size(files))[[1]]])
   
   if (!length(files)) 
     stop("Score results not found.", call. = FALSE)
@@ -1551,6 +1561,12 @@ calc_pepfdr <- function (target_fdr = .01, fdr_type = "psm",
       td[td[["pep_mod_group"]] == max_i & grepl("[KR]$", td[["pep_seq"]]), ]
     else if (nes_fdr_group == "base_cterm_nontryptic")
       td[td[["pep_mod_group"]] == max_i & !grepl("[KR]$", td[["pep_seq"]]), ]
+    else if (nes_fdr_group == "top3")
+      td[td[["pep_mod_group"]] %in% top3s, ]
+    else if (nes_fdr_group == "top3_cterm_tryptic")
+      td[td[["pep_mod_group"]] %in% top3s & grepl("[KR]$", td[["pep_seq"]]), ]
+    else if (nes_fdr_group == "top3_cterm_nontryptic")
+      td[td[["pep_mod_group"]] %in% top3s & !grepl("[KR]$", td[["pep_seq"]]), ]
     else
       stop("Invalid argument for \"nes_fdr_group\".")
   }
@@ -1559,6 +1575,8 @@ calc_pepfdr <- function (target_fdr = .01, fdr_type = "psm",
       td
     else if (fdr_group == "base")
       td[td[["pep_mod_group"]] == max_i, ]
+    else if (fdr_group == "top3")
+      td[td[["pep_mod_group"]] %in% top3s, ]
     else 
       stop("Invalid argument for \"fdr_group\".")
   }
@@ -1600,7 +1618,6 @@ calc_pepfdr <- function (target_fdr = .01, fdr_type = "psm",
   td <- dplyr::arrange(td, pep_prob)
   td <- dplyr::filter(td, row_number() == 1L)
   td <- dplyr::ungroup(td)
-  
   gc()
   
   # --- 
@@ -1625,7 +1642,7 @@ calc_pepfdr <- function (target_fdr = .01, fdr_type = "psm",
     return(data.frame(pep_len = seqs, pep_prob_co = prob_cos))
   } 
   
-  counts <- as.numeric(names(prob_cos))
+  counts <- as.integer(names(prob_cos))
   names(counts) <- all_lens
   names(prob_cos) <- all_lens
   
@@ -1643,7 +1660,7 @@ calc_pepfdr <- function (target_fdr = .01, fdr_type = "psm",
   # (At least two non-trivial prob_cos)
   #########################################
   
-  lens <- find_optlens(all_lens, counts, 128L)
+  lens <- find_optlens(all_lens, counts, 50L) # changed from 128L
   
   # no fittings
   if (length(lens) <= 3L) {
@@ -2428,8 +2445,8 @@ match_ex2th2 <- function (expt, theo, min_ms2mass = 115L, d = 1E-5,
 {
   th <- index_mz(theo, from = min_ms2mass, d = d)
   ex <- if (index_mgf_ms2) expt else index_mz(expt, from = min_ms2mass, d = d)
-  ith <- which(th %fin% ex | (th - 1L) %fin% ex | (th + 1L) %fin% ex)
-  
+  ith <- .Internal(which(th %fin% ex | (th - 1L) %fin% ex | (th + 1L) %fin% ex))
+
   # if: e.g. th[ith+1] = th[ith] + 1 -> can have NA in iex:
   #   th[ith+1] not in ex but th[ith+1] - 1
   # OK to keep the NA:
@@ -2441,7 +2458,7 @@ match_ex2th2 <- function (expt, theo, min_ms2mass = 115L, d = 1E-5,
   iex <- fastmatch::fmatch(thi, ex)
   
   # indexes before and after
-  nas <- which(is.na(iex))
+  nas <- .Internal(which(is.na(iex)))
   
   if (length(nas)) {
     bf <- fastmatch::fmatch(thi - 1L, ex)
@@ -2452,8 +2469,8 @@ match_ex2th2 <- function (expt, theo, min_ms2mass = 115L, d = 1E-5,
     }
     else {
       iex[nas] <- bf[nas]
-      nas <- which(is.na(iex))
-      
+      nas <- .Internal(which(is.na(iex)))
+
       if (length(nas)) {
         af <- fastmatch::fmatch(thi + 1L, ex)
         iex[nas] <- af[nas]
diff --git a/R/utils_engine.R b/R/utils_engine.R
index 7c6f426..9ca199a 100644
--- a/R/utils_engine.R
+++ b/R/utils_engine.R
@@ -26,7 +26,7 @@ which_topx <- function(x, n = 50L, ...)
   
   xp <- sort(x, partial = p, ...)[p]
   
-  which(x > xp)
+  .Internal(which(x > xp))
 }
 
 
@@ -85,8 +85,8 @@ which_topx2 <- function(x, n = 50L, ...)
   # or:  xp <- sort(x, partial = p, na.last = TRUE)[p]
   xp <- sort(x, partial = p, ...)[p]
   
-  inds <- which(x > xp)
-  
+  inds <- .Internal(which(x > xp))
+
   # in case of ties -> length(inds) < n
   # detrimental e.g. ms2_n = 500 and n = 100
   #   -> expect 100 `ms2_moverzs` guaranteed but may be only 99
@@ -98,7 +98,7 @@ which_topx2 <- function(x, n = 50L, ...)
   
   if (d) {
     # must exist and length(ties) >= length(d)
-    ties <- which(x == xp)
+    ties <- .Internal(which(x == xp))
     for (i in seq_len(d)) inds <- insVal(ties[i], inds)
   }
   
@@ -253,11 +253,11 @@ purge_search_space <- function (i, aa_masses, mgf_path, n_cores, ppm_ms1 = 10L,
                                 fmods_nl = NULL) 
 {
   # loads freshly mgfs (as will be modified)
-  mgf_frames <- 
-    qs::qread(file.path(mgf_path, "mgf_queries.rds")) %>% 
-    dplyr::group_by(frame) %>%
-    dplyr::group_split() %>%
-    setNames(purrr::map_dbl(., function (x) x$frame[1]))
+  mgf_frames <- qs::qread(file.path(mgf_path, "mgf_queries.rds"))
+  mgf_frames <- dplyr::group_by(mgf_frames, frame)
+  mgf_frames <- dplyr::group_split(mgf_frames)
+  frs <- lapply(mgf_frames, function (x) x[["frame"]][1])
+  names(mgf_frames) <- unlist(frs, recursive = FALSE, use.names = FALSE)
 
   mgf_frames <- local({
     ranges <- seq_along(mgf_frames)
@@ -270,12 +270,8 @@ purge_search_space <- function (i, aa_masses, mgf_path, n_cores, ppm_ms1 = 10L,
   # parses aa_masses
   nm_fmods <- attr(aa_masses, "fmods", exact = TRUE)
   nm_vmods <- attr(aa_masses, "vmods", exact = TRUE)
-  msg_end  <- if (grepl("^rev_", i)) " (decoy)." else "."
-
-  message("Matching against: ",
-          paste0(nm_fmods,
-                 nm_vmods %>% { if (nchar(.) > 0L) paste0(" | ", .) else . },
-                 msg_end))
+  message("Matching against: ", 
+          if (nchar(nm_vmods) == 0L) nm_fmods else paste0(nm_fmods, " | ", nm_vmods))
 
   # reads theoretical peptide data
   .path_bin <- get(".path_bin", envir = .GlobalEnv, inherits = FALSE)
@@ -294,8 +290,10 @@ purge_search_space <- function (i, aa_masses, mgf_path, n_cores, ppm_ms1 = 10L,
     oks <- names(x) %fin% frames_theo
     x <- x[oks]
     
-    empties <- purrr::map_lgl(x, purrr::is_empty)
-    x[!empties]
+    ans <- .Internal(unlist(lapply(x, function (y) length(x) > 0L), 
+                            recursive = FALSE, use.names = FALSE))
+    
+    x[ans]
   })
   
   rm(list = "frames_theo")
@@ -304,11 +302,11 @@ purge_search_space <- function (i, aa_masses, mgf_path, n_cores, ppm_ms1 = 10L,
   #     preceding and following frames: (o)|range of mgf_frames[[1]]|(o)
   frames_mgf <- lapply(mgf_frames, function (x) as.integer(names(x)))
   
-  mins <- purrr::map_int(frames_mgf, function (x) 
-    if (length(x)) min(x, na.rm = TRUE) else 0L)
+  mins <- lapply(frames_mgf, function (x) if (length(x)) min(x, na.rm = TRUE) else 0L)
+  mins <- .Internal(unlist(mins, recursive = FALSE, use.names = FALSE))
 
-  maxs <- purrr::map_int(frames_mgf, function (x) 
-    if (length(x)) max(x, na.rm = TRUE) else 0L)
+  maxs <- lapply(frames_mgf, function (x) if (length(x)) max(x, na.rm = TRUE) else 0L)
+  maxs <- .Internal(unlist(maxs, recursive = FALSE, use.names = FALSE))
 
   frames_theo <- as.integer(names(theopeps))
   
@@ -329,9 +327,11 @@ purge_search_space <- function (i, aa_masses, mgf_path, n_cores, ppm_ms1 = 10L,
                      SIMPLIFY = FALSE, USE.NAMES = FALSE)
 
   # (4) removes empties (zero overlap between mgf_frames and theopeps)
-  oks <- purrr::map_lgl(mgf_frames, function (x) length(x) > 0L) |
-    purrr::map_lgl(theopeps, function (x) length(x) > 0L)
-
+  ok_mgfs <- lapply(mgf_frames, function (x) length(x) > 0L)
+  ok_mgfs <- .Internal(unlist(ok_mgfs, recursive = FALSE, use.names = FALSE))
+  ok_theos <- lapply(theopeps, function (x) length(x) > 0L)
+  ok_theos <- .Internal(unlist(ok_theos, recursive = FALSE, use.names = FALSE))
+  oks <- ok_mgfs | ok_theos
   mgf_frames <- mgf_frames[oks]
   theopeps <- theopeps[oks]
 
diff --git a/man/add_hexcodes_vnl2.Rd b/man/add_hexcodes_vnl2.Rd
index 5277a5d..fcdc41a 100644
--- a/man/add_hexcodes_vnl2.Rd
+++ b/man/add_hexcodes_vnl2.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/ms2_a1_vnl1_fnl0.R
 \name{add_hexcodes_vnl2}
 \alias{add_hexcodes_vnl2}
-\title{Adds hex codes (with variable NLs).}
+\title{Adds hexcodes (with variable NLs).}
 \usage{
 add_hexcodes_vnl2(ms2ions, vmods_combi, len, mod_indexes = NULL)
 }
diff --git a/man/add_protacc.Rd b/man/add_protacc.Rd
index 6df8132..3c7b04b 100644
--- a/man/add_protacc.Rd
+++ b/man/add_protacc.Rd
@@ -12,14 +12,10 @@ add_protacc(df = NULL, out_path = NULL, .path_cache = NULL, .path_fasta = NULL)
 \item{out_path}{An output path.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{.path_fasta}{The parent file path to the theoretical masses of MS1
 precursors. At the NULL default, the path is \code{gsub("(.*)\\.[^\\.]*$",
diff --git a/man/add_protacc2.Rd b/man/add_protacc2.Rd
index 41aa213..6362d73 100644
--- a/man/add_protacc2.Rd
+++ b/man/add_protacc2.Rd
@@ -17,14 +17,10 @@ add_protacc2(
 \item{out_path}{An output path.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{.path_fasta}{The parent file path to the theoretical masses of MS1
 precursors. At the NULL default, the path is \code{gsub("(.*)\\.[^\\.]*$",
diff --git a/man/batch_ms2ions.Rd b/man/batch_ms2ions.Rd
index 1d5cf29..291016f 100644
--- a/man/batch_ms2ions.Rd
+++ b/man/batch_ms2ions.Rd
@@ -64,14 +64,10 @@ number of combinatorial variable modifications per peptide sequence. The
 default is 64.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{.path_fasta}{The parent file path to the theoretical masses of MS1
 precursors. At the NULL default, the path is \code{gsub("(.*)\\.[^\\.]*$",
diff --git a/man/bin_ms1masses.Rd b/man/bin_ms1masses.Rd
index 1256f41..482f01d 100644
--- a/man/bin_ms1masses.Rd
+++ b/man/bin_ms1masses.Rd
@@ -34,14 +34,10 @@ default is 20.}
   \code{fdr_type = psm} to \code{fdr_type = protein}.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{.path_ms1masses}{The file path to the theoretical masses of MS1
 precursors.}
diff --git a/man/calc_pepfdr.Rd b/man/calc_pepfdr.Rd
index 869998f..93ca125 100644
--- a/man/calc_pepfdr.Rd
+++ b/man/calc_pepfdr.Rd
@@ -6,14 +6,14 @@
 \usage{
 calc_pepfdr(
   target_fdr = 0.01,
-  fdr_type = "psm",
+  fdr_type = "protein",
   min_len = 7L,
   max_len = 40L,
   max_pepscores_co = 50,
   min_pepscores_co = 0,
   enzyme = "trypsin_p",
-  fdr_group = "all",
-  nes_fdr_group = "all",
+  fdr_group = "base",
+  nes_fdr_group = "base",
   out_path
 )
 }
@@ -30,8 +30,7 @@ for considerations. Longer peptides will be excluded.}
 
 \item{max_pepscores_co}{A positive numeric; the upper limit in the cut-offs
 of peptide scores for discriminating significant and insignificant
-identities. The default is changed from \code{Inf} to 50 from version
-1.1.9.2 on.}
+identities.}
 
 \item{min_pepscores_co}{A non-negative numeric; the lower limit in the
 cut-offs of peptide scores for discriminating significant and insignificant
diff --git a/man/calc_pepmasses2.Rd b/man/calc_pepmasses2.Rd
index 08845db..62a2dd4 100644
--- a/man/calc_pepmasses2.Rd
+++ b/man/calc_pepmasses2.Rd
@@ -154,14 +154,10 @@ time.}
   \code{fdr_type = psm} to \code{fdr_type = protein}.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{.path_fasta}{The parent file path to the theoretical masses of MS1
 precursors. At the NULL default, the path is \code{gsub("(.*)\\.[^\\.]*$",
diff --git a/man/calc_pepprobs_i.Rd b/man/calc_pepprobs_i.Rd
index 2903c28..c4bc09e 100644
--- a/man/calc_pepprobs_i.Rd
+++ b/man/calc_pepprobs_i.Rd
@@ -31,10 +31,10 @@ and y-ions.}
 \item{ppm_ms2}{A positive integer; the mass tolerance of MS2 species. The
 default is 20.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{out_path}{A file path of outputs.}
 
diff --git a/man/calc_pepscores.Rd b/man/calc_pepscores.Rd
index a0a1c33..ec00e44 100644
--- a/man/calc_pepscores.Rd
+++ b/man/calc_pepscores.Rd
@@ -8,7 +8,7 @@ calc_pepscores(
   topn_ms2ions = 100L,
   type_ms2ions = "by",
   target_fdr = 0.01,
-  fdr_type = "psm",
+  fdr_type = "protein",
   min_len = 7L,
   max_len = 40L,
   ppm_ms2 = 20L,
@@ -55,7 +55,7 @@ levels of PSM, peptide or protein. The default is 0.01. See also argument
 \item{fdr_type}{A character string; the type of FDR control. The value is in
   one of c("protein", "peptide", "psm"). The default is \code{protein}.
 
-  Note that \code{fdr_type = protein} is equivalent to \code{fdr_type =
+  Note that \code{fdr_type = protein} is comparable to \code{fdr_type =
   peptide} with the additional filtration of data at \code{prot_tier == 1}.}
 
 \item{min_len}{A positive integer; the minimum length of peptide sequences
@@ -67,10 +67,10 @@ for considerations. Longer peptides will be excluded.}
 \item{ppm_ms2}{A positive integer; the mass tolerance of MS2 species. The
 default is 20.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{out_path}{A file path of outputs.}
 
diff --git a/man/calc_probi.Rd b/man/calc_probi.Rd
index 7ffd6d4..ed32e48 100644
--- a/man/calc_probi.Rd
+++ b/man/calc_probi.Rd
@@ -39,10 +39,10 @@ searches.}
 \item{ppm_ms2}{A positive integer; the mass tolerance of MS2 species. The
 default is 20.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{min_ms2mass}{A positive integer; the minimum MS2 mass for
 interrogation. The default is 110.}
diff --git a/man/calc_probi_bypep.Rd b/man/calc_probi_bypep.Rd
index 6e518a3..ba2ed56 100644
--- a/man/calc_probi_bypep.Rd
+++ b/man/calc_probi_bypep.Rd
@@ -42,10 +42,10 @@ searches.}
 \item{ppm_ms2}{A positive integer; the mass tolerance of MS2 species. The
 default is 20.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{min_ms2mass}{A positive integer; the minimum MS2 mass for
 interrogation. The default is 110.}
diff --git a/man/calc_probi_byvmods.Rd b/man/calc_probi_byvmods.Rd
index c4d940d..ab31f8a 100644
--- a/man/calc_probi_byvmods.Rd
+++ b/man/calc_probi_byvmods.Rd
@@ -44,10 +44,10 @@ searches.}
 \item{ppm_ms2}{A positive integer; the mass tolerance of MS2 species. The
 default is 20.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{burn_ins}{The range of burn-ins where inputs will be excluded from
 probablity assessments.}
diff --git a/man/calcpepsc.Rd b/man/calcpepsc.Rd
index 267d62f..33316c7 100644
--- a/man/calcpepsc.Rd
+++ b/man/calcpepsc.Rd
@@ -18,6 +18,7 @@ calcpepsc(
   add_ms2theos2 = FALSE,
   add_ms2moverzs = FALSE,
   add_ms2ints = FALSE,
+  n_cores = 16L,
   digits = 4L
 )
 }
@@ -35,10 +36,10 @@ and y-ions.}
 \item{ppm_ms2}{A positive integer; the mass tolerance of MS2 species. The
 default is 20.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{out_path}{A file path of outputs.}
 
@@ -82,6 +83,8 @@ interrogation. The default is 110.}
 \item{add_ms2ints}{Logical; if TRUE, adds the sequence of experimental MS2
 intensity values (\code{pep_ms2_ints}).}
 
+\item{n_cores}{The number of CPU cores.}
+
 \item{digits}{A non-negative integer; the number of decimal places to be
 used. The default is 4.}
 }
diff --git a/man/check_fdr_group.Rd b/man/check_fdr_group.Rd
new file mode 100644
index 0000000..98cb5c2
--- /dev/null
+++ b/man/check_fdr_group.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/msmsmatches.R
+\name{check_fdr_group}
+\alias{check_fdr_group}
+\title{Checks the values of \code{fdr_group}}
+\usage{
+check_fdr_group(fdr_group = c("base", "all", "top3"), oks = c("base", "all"))
+}
+\arguments{
+\item{fdr_group}{A character string; the modification group(s) for uses in
+peptide FDR controls. The value is in one of c("all", "base"). The
+\code{base} corresponds to the modification group with the largest number
+of matches.}
+}
+\description{
+Not yet used. Takes values of integers or character strings.
+}
diff --git a/man/check_ms2frames.Rd b/man/check_ms2frames.Rd
index 3e04e08..495a7a6 100644
--- a/man/check_ms2frames.Rd
+++ b/man/check_ms2frames.Rd
@@ -23,14 +23,10 @@ developer.}
 \item{ms1_time}{A cached MS1 time (directory).}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{path_bin2}{A file path to binned MS2 results.}
 }
diff --git a/man/hbatch_ms2ions.Rd b/man/hbatch_ms2ions.Rd
index b286876..2cf9f89 100644
--- a/man/hbatch_ms2ions.Rd
+++ b/man/hbatch_ms2ions.Rd
@@ -42,14 +42,10 @@ number of combinatorial variable modifications per peptide sequence. The
 default is 64.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{.path_fasta}{The parent file path to the theoretical masses of MS1
 precursors. At the NULL default, the path is \code{gsub("(.*)\\.[^\\.]*$",
diff --git a/man/load_fasta2.Rd b/man/load_fasta2.Rd
index 956158a..c430e7f 100644
--- a/man/load_fasta2.Rd
+++ b/man/load_fasta2.Rd
@@ -29,30 +29,26 @@ otherwise, the first value will be used for all \code{fasta} files.
 fasta_db <- load_fasta2(
               c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
                 "~/proteoM/dbs/fasta/crap/crap.fasta"),
-              c("uniprot_acc", "other")
-)
+              c("uniprot_acc", "other"))
 
 # Need `acc_pattern` as "crap" is not one of the default acc_type
 load_fasta2(
    c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
      "~/proteoM/dbs/fasta/crap/crap.fasta"),
-   c("uniprot_acc", "crap")
-)
+   c("uniprot_acc", "crap"))
 
 # ok
 fasta_db2 <- load_fasta2(
                c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
                  "~/proteoM/dbs/fasta/crap/crap.fasta"),
                c("uniprot_acc", "crap"),
-               c("^>..\\\\|([^\\\\|]+)\\\\|[^\\\\|]+", "(.*)")
-)
+               c("^>..\\\\|([^\\\\|]+)\\\\|[^\\\\|]+", "(.*)"))
 
 fasta_db3 <- load_fasta2(
                c("~/proteoM/dbs/fasta/uniprot/uniprot_hs_2020_05.fasta",
                  "~/proteoM/dbs/fasta/crap/crap.fasta"),
                c("my_acc", "crap"),
-               c("^>..\\\\|([^\\\\|]+)\\\\|[^\\\\|]+", "(.*)")
-)
+               c("^>..\\\\|([^\\\\|]+)\\\\|[^\\\\|]+", "(.*)"))
 
 stopifnot(identical(fasta_db, fasta_db2),
           identical(fasta_db, fasta_db3))
diff --git a/man/make_ms2frames.Rd b/man/make_ms2frames.Rd
index 8502287..9abdec5 100644
--- a/man/make_ms2frames.Rd
+++ b/man/make_ms2frames.Rd
@@ -22,14 +22,10 @@ masses in values.}
 \item{ms2s}{Lists of MS2 ion series.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{path_bin2}{A file path to binned MS2 results.}
 
diff --git a/man/matchMS.Rd b/man/matchMS.Rd
index 5fbef33..d655cd4 100644
--- a/man/matchMS.Rd
+++ b/man/matchMS.Rd
@@ -23,15 +23,16 @@ matchMS(
     "SemiLysN", "SemiArgC", "SemiLysC_P", "SemiChymotrypsin", "SemiGluC", "SemiGluN",
     "SemiAspC", "SemiAspN", "Noenzyme", "Nodigest"),
   custom_enzyme = c(Cterm = NULL, Nterm = NULL),
-  nes_fdr_group = c("all", "all_cterm_tryptic", "all_cterm_nontryptic", "base",
-    "base_cterm_tryptic", "base_cterm_nontryptic"),
+  nes_fdr_group = c("base", "base_cterm_tryptic", "base_cterm_nontryptic", "all",
+    "all_cterm_tryptic", "all_cterm_nontryptic", "top3", "top3_cterm_tryptic",
+    "top3_cterm_nontryptic"),
   noenzyme_maxn = 0L,
   maxn_fasta_seqs = 200000L,
   maxn_vmods_setscombi = 512L,
   maxn_vmods_per_pep = 5L,
   maxn_sites_per_vmod = 3L,
-  maxn_fnl_per_seq = 64L,
-  maxn_vnl_per_seq = 64L,
+  maxn_fnl_per_seq = 8L,
+  maxn_vnl_per_seq = 8L,
   maxn_vmods_sitescombi_per_pep = 64L,
   min_len = 7L,
   max_len = 40L,
@@ -55,7 +56,7 @@ matchMS(
   quant = c("none", "tmt6", "tmt10", "tmt11", "tmt16", "tmt18"),
   target_fdr = 0.01,
   fdr_type = c("protein", "peptide", "psm"),
-  fdr_group = c("all", "base"),
+  fdr_group = c("base", "all", "top3"),
   max_pepscores_co = 50,
   min_pepscores_co = 0,
   max_protscores_co = Inf,
@@ -333,7 +334,7 @@ levels of PSM, peptide or protein. The default is 0.01. See also argument
 \item{fdr_type}{A character string; the type of FDR control. The value is in
   one of c("protein", "peptide", "psm"). The default is \code{protein}.
 
-  Note that \code{fdr_type = protein} is equivalent to \code{fdr_type =
+  Note that \code{fdr_type = protein} is comparable to \code{fdr_type =
   peptide} with the additional filtration of data at \code{prot_tier == 1}.}
 
 \item{fdr_group}{A character string; the modification group(s) for uses in
@@ -343,8 +344,7 @@ of matches.}
 
 \item{max_pepscores_co}{A positive numeric; the upper limit in the cut-offs
 of peptide scores for discriminating significant and insignificant
-identities. The default is changed from \code{Inf} to 50 from version
-1.1.9.2 on.}
+identities.}
 
 \item{min_pepscores_co}{A non-negative numeric; the lower limit in the
 cut-offs of peptide scores for discriminating significant and insignificant
@@ -371,10 +371,10 @@ pep_score_cutoff} under a protein will be used to represent the threshold
 of a protein enrichment score. For more conserved thresholds, the
 statistics of \code{"max"} may be considered.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{topn_mods_per_seq}{Positive integer; a threshold to discard variable
   modifications under the same peptide match with scores beyond the top-n.
@@ -393,17 +393,19 @@ For instance, the signal of \code{b5^*} will be ignored if its primary ion
   and \code{MS raw file name}. Target and decoys matches are treated
   separately.}
 
-\item{combine_tier_three}{Logical; if TRUE, combines search results at tiers
-  1, 2 and 3 to the single output of \code{psmQ.txt}. The default is FALSE in
-  that data will be segregated into the three quality tiers according to the
-  choice of \code{fdr_type}. The (convenience) parameter matters since
-  \href{http://github.com/qzhang503/proteoQ}{proteoQ} will only look for the
-  inputs of \code{psmQ[...].txt}.
-
-  For instance, if the aim is to bypass the constraint by protein FDR and
-  focus on PSMs that have met the cut-offs specified by \code{target_fdr}, an
-  experimenter may set \code{combine_tier_three = TRUE} and hence pool all
-  significant peptides in \code{psmQ.txt} for downstream proteoQ.
+\item{combine_tier_three}{Logical; if TRUE, combines search results at tier-3
+  to tier-1 to form the single output of \code{psmQ.txt}. The default is
+  FALSE in that data will be segregated into the three quality tiers shown
+  below by the choice of \code{fdr_type}. Note that the argument affects only
+  at the \code{fdr_type} of \code{psm} or \code{peptide} and there is no
+  tier-2 outputs at the \code{fdr_type} of \code{psm} or \code{peptide}. In
+  general, the one-hit-wonders from the tier-3 should not be used.
+  
+  In subproteome analysis, such as phosphoproteome analysis, some proteins
+  may be well established globally, but fail the significance assessment by
+  protein FDR on the local scale. In situations like this, it may be suitable
+  to use \code{fdr_type = "peptide"} or \code{fdr_type = "psm"} and not to
+  incur \code{combine_tier_three = TRUE}.
 
   Tier-1: both proteins and peptides with scores above significance
   thresholds.
@@ -433,14 +435,10 @@ For instance, the signal of \code{b5^*} will be ignored if its primary ion
   \code{fdr_type = psm} to \code{fdr_type = protein}.}
 
 \item{.path_cache}{The file path of cached search parameters. The parameter
-  is for the users' awareness of the underlying structure of file folders and
-  the use of default is suggested. Occasionally experimenters may remove the
-  file folder for disk space or under infrequent events of modified framework
-  incurred by the developer.
-
-  Started from version 1.2.1.5, a new data structure of protein-peptide
-  lookups are used. Version 1.2.1.4.1 is the final version using the old data
-  structure.}
+is for the users' awareness of the underlying structure of file folders and
+the use of default is suggested. Occasionally experimenters may remove the
+file folder for disk space or under infrequent events of modified framework
+incurred by the developer.}
 
 \item{.path_fasta}{The parent file path to the theoretical masses of MS1
 precursors. At the NULL default, the path is \code{gsub("(.*)\\.[^\\.]*$",
diff --git a/man/probco_bypeplen.Rd b/man/probco_bypeplen.Rd
index 45d3d19..7b691c2 100644
--- a/man/probco_bypeplen.Rd
+++ b/man/probco_bypeplen.Rd
@@ -7,7 +7,7 @@
 probco_bypeplen(
   len,
   td,
-  fdr_type = "psm",
+  fdr_type = "protein",
   target_fdr = 0.01,
   min_pepscores_co = 0,
   out_path
@@ -21,7 +21,7 @@ probco_bypeplen(
 \item{fdr_type}{A character string; the type of FDR control. The value is in
   one of c("protein", "peptide", "psm"). The default is \code{protein}.
 
-  Note that \code{fdr_type = protein} is equivalent to \code{fdr_type =
+  Note that \code{fdr_type = protein} is comparable to \code{fdr_type =
   peptide} with the additional filtration of data at \code{prot_tier == 1}.}
 
 \item{target_fdr}{A numeric; the targeted false-discovery rate (FDR) at the
diff --git a/man/psmC2Q.Rd b/man/psmC2Q.Rd
index db54803..e1350f9 100644
--- a/man/psmC2Q.Rd
+++ b/man/psmC2Q.Rd
@@ -22,20 +22,22 @@ or decoy peptides, as well as decoy proteins.}
 \item{fdr_type}{A character string; the type of FDR control. The value is in
   one of c("protein", "peptide", "psm"). The default is \code{protein}.
 
-  Note that \code{fdr_type = protein} is equivalent to \code{fdr_type =
+  Note that \code{fdr_type = protein} is comparable to \code{fdr_type =
   peptide} with the additional filtration of data at \code{prot_tier == 1}.}
 
-\item{combine_tier_three}{Logical; if TRUE, combines search results at tiers
-  1, 2 and 3 to the single output of \code{psmQ.txt}. The default is FALSE in
-  that data will be segregated into the three quality tiers according to the
-  choice of \code{fdr_type}. The (convenience) parameter matters since
-  \href{http://github.com/qzhang503/proteoQ}{proteoQ} will only look for the
-  inputs of \code{psmQ[...].txt}.
-
-  For instance, if the aim is to bypass the constraint by protein FDR and
-  focus on PSMs that have met the cut-offs specified by \code{target_fdr}, an
-  experimenter may set \code{combine_tier_three = TRUE} and hence pool all
-  significant peptides in \code{psmQ.txt} for downstream proteoQ.
+\item{combine_tier_three}{Logical; if TRUE, combines search results at tier-3
+  to tier-1 to form the single output of \code{psmQ.txt}. The default is
+  FALSE in that data will be segregated into the three quality tiers shown
+  below by the choice of \code{fdr_type}. Note that the argument affects only
+  at the \code{fdr_type} of \code{psm} or \code{peptide} and there is no
+  tier-2 outputs at the \code{fdr_type} of \code{psm} or \code{peptide}. In
+  general, the one-hit-wonders from the tier-3 should not be used.
+  
+  In subproteome analysis, such as phosphoproteome analysis, some proteins
+  may be well established globally, but fail the significance assessment by
+  protein FDR on the local scale. In situations like this, it may be suitable
+  to use \code{fdr_type = "peptide"} or \code{fdr_type = "psm"} and not to
+  incur \code{combine_tier_three = TRUE}.
 
   Tier-1: both proteins and peptides with scores above significance
   thresholds.
diff --git a/man/reproc_psmC.Rd b/man/reproc_psmC.Rd
index eb7de3c..c961538 100644
--- a/man/reproc_psmC.Rd
+++ b/man/reproc_psmC.Rd
@@ -18,20 +18,22 @@ reproc_psmC(
 \item{fdr_type}{A character string; the type of FDR control. The value is in
   one of c("protein", "peptide", "psm"). The default is \code{protein}.
 
-  Note that \code{fdr_type = protein} is equivalent to \code{fdr_type =
+  Note that \code{fdr_type = protein} is comparable to \code{fdr_type =
   peptide} with the additional filtration of data at \code{prot_tier == 1}.}
 
-\item{combine_tier_three}{Logical; if TRUE, combines search results at tiers
-  1, 2 and 3 to the single output of \code{psmQ.txt}. The default is FALSE in
-  that data will be segregated into the three quality tiers according to the
-  choice of \code{fdr_type}. The (convenience) parameter matters since
-  \href{http://github.com/qzhang503/proteoQ}{proteoQ} will only look for the
-  inputs of \code{psmQ[...].txt}.
-
-  For instance, if the aim is to bypass the constraint by protein FDR and
-  focus on PSMs that have met the cut-offs specified by \code{target_fdr}, an
-  experimenter may set \code{combine_tier_three = TRUE} and hence pool all
-  significant peptides in \code{psmQ.txt} for downstream proteoQ.
+\item{combine_tier_three}{Logical; if TRUE, combines search results at tier-3
+  to tier-1 to form the single output of \code{psmQ.txt}. The default is
+  FALSE in that data will be segregated into the three quality tiers shown
+  below by the choice of \code{fdr_type}. Note that the argument affects only
+  at the \code{fdr_type} of \code{psm} or \code{peptide} and there is no
+  tier-2 outputs at the \code{fdr_type} of \code{psm} or \code{peptide}. In
+  general, the one-hit-wonders from the tier-3 should not be used.
+  
+  In subproteome analysis, such as phosphoproteome analysis, some proteins
+  may be well established globally, but fail the significance assessment by
+  protein FDR on the local scale. In situations like this, it may be suitable
+  to use \code{fdr_type = "peptide"} or \code{fdr_type = "psm"} and not to
+  incur \code{combine_tier_three = TRUE}.
 
   Tier-1: both proteins and peptides with scores above significance
   thresholds.
diff --git a/man/scalc_pepprobs.Rd b/man/scalc_pepprobs.Rd
index da17950..b637417 100644
--- a/man/scalc_pepprobs.Rd
+++ b/man/scalc_pepprobs.Rd
@@ -30,10 +30,10 @@ and y-ions.}
 \item{ppm_ms2}{A positive integer; the mass tolerance of MS2 species. The
 default is 20.}
 
-\item{soft_secions}{Logical; if TRUE, collapses the intensities of secondary
-ions to primary ions at the absence of the primaries. The default is FALSE.
-For instance, the signal of \code{b5^*} will be ignored if its primary ion
-\code{b5} is not matched.}
+\item{soft_secions}{Depreciated. Logical; if TRUE, collapses the intensities
+of secondary ions to primary ions at the absence of the primaries. The
+default is FALSE. For instance, the signal of \code{b5^*} will be ignored
+if its primary ion \code{b5} is not matched.}
 
 \item{min_ms2mass}{A positive integer; the minimum MS2 mass for
 interrogation. The default is 110.}
diff --git a/man/try_psmC2Q.Rd b/man/try_psmC2Q.Rd
index 9345c45..c6c7844 100644
--- a/man/try_psmC2Q.Rd
+++ b/man/try_psmC2Q.Rd
@@ -21,20 +21,22 @@ or decoy peptides, as well as decoy proteins.}
 \item{fdr_type}{A character string; the type of FDR control. The value is in
   one of c("protein", "peptide", "psm"). The default is \code{protein}.
 
-  Note that \code{fdr_type = protein} is equivalent to \code{fdr_type =
+  Note that \code{fdr_type = protein} is comparable to \code{fdr_type =
   peptide} with the additional filtration of data at \code{prot_tier == 1}.}
 
-\item{combine_tier_three}{Logical; if TRUE, combines search results at tiers
-  1, 2 and 3 to the single output of \code{psmQ.txt}. The default is FALSE in
-  that data will be segregated into the three quality tiers according to the
-  choice of \code{fdr_type}. The (convenience) parameter matters since
-  \href{http://github.com/qzhang503/proteoQ}{proteoQ} will only look for the
-  inputs of \code{psmQ[...].txt}.
-
-  For instance, if the aim is to bypass the constraint by protein FDR and
-  focus on PSMs that have met the cut-offs specified by \code{target_fdr}, an
-  experimenter may set \code{combine_tier_three = TRUE} and hence pool all
-  significant peptides in \code{psmQ.txt} for downstream proteoQ.
+\item{combine_tier_three}{Logical; if TRUE, combines search results at tier-3
+  to tier-1 to form the single output of \code{psmQ.txt}. The default is
+  FALSE in that data will be segregated into the three quality tiers shown
+  below by the choice of \code{fdr_type}. Note that the argument affects only
+  at the \code{fdr_type} of \code{psm} or \code{peptide} and there is no
+  tier-2 outputs at the \code{fdr_type} of \code{psm} or \code{peptide}. In
+  general, the one-hit-wonders from the tier-3 should not be used.
+  
+  In subproteome analysis, such as phosphoproteome analysis, some proteins
+  may be well established globally, but fail the significance assessment by
+  protein FDR on the local scale. In situations like this, it may be suitable
+  to use \code{fdr_type = "peptide"} or \code{fdr_type = "psm"} and not to
+  incur \code{combine_tier_three = TRUE}.
 
   Tier-1: both proteins and peptides with scores above significance
   thresholds.